Structural Classification of Proteins

Class: All alpha proteins

Lineage:

Root: scop
Class: All alpha proteins [46456]

Folds:

Globin-like [46457] (2)
core: 6 helices; folded leaf, partly opened
1. Globin-like [46458] (4)
  uperfamily
  1. Truncated hemoglobin [46459] (6)
    lack the first helix (A)
  2. Nerve tissue mini-hemoglobin (neural globin) [74660] (1)
    lack the first helix but otherwise is more similar to conventional globins than the truncated ones
  3. Globins [46463] (81)
    Heme-binding protein
  4. Phycocyanin-like phycobilisome proteins [46532] (26)
    oligomers of two different types of globin-like subunits containing two extra helices at the N-terminus
    binds a bilin chromophore
2. alpha-helical ferredoxin [46548] (2)
  contains two Fe4-S4 clusters
  uperfamily
  1. Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain [46549] (3)
  2. Dihydropyrimidine dehydrogenase, N-terminal domain [46553] (1)
Long alpha-hairpin [46556] (20)
2 helices; antiparallel hairpin, left-handed twist
1. GreA transcript cleavage protein, N-terminal domain [46557] (1)
  uperfamily
  1. GreA transcript cleavage protein, N-terminal domain [46558] (3)
2. Ribosomal protein L29 (L29p) [46561] (1)
  uperfamily
  1. Ribosomal protein L29 (L29p) [46562] (5)
3. Chaperone J-domain [46565] (1)
  uperfamily
  1. Chaperone J-domain [46566] (8)
    Pfam 00226
4. Prefoldin [46579] (1)
  uperfamily
  1. Prefoldin [46580] (2)
    contains one or two beta-hairpins at the tip of alpha-hairpin
5. HR1 repeat [46585] (1)
  uperfamily
  1. HR1 repeat [46586] (1)
    protein kinase effector domain
6. tRNA-binding arm [46589] (4)
  formerly a class II aminoacyl-tRNA synthetase N-domain
  uperfamily
  1. Seryl-tRNA synthetase (SerRS) [46590] (1)
  2. Phenylalanyl-tRNA synthetase (PheRS) [46593] (1)
  3. Valyl-tRNA synthetase (ValRS) C-terminal domain [81635] (1)
  4. Methicillin resistance protein FemA probable tRNA-binding arm [81671] (1)
    inserted in the C-terminal NAT-like domain
7. Eukaryotic DNA topoisomerase I, dispensable insert domain [46596] (1)
  uperfamily
  1. Eukaryotic DNA topoisomerase I, dispensable insert domain [46597] (1)
8. C-terminal UvrC-binding domain of UvrB [46600] (1)
  uperfamily
  1. C-terminal UvrC-binding domain of UvrB [46601] (1)
9. Epsilon subunit of F1F0-ATP synthase C-terminal domain [46604] (1)
  uperfamily
  1. Epsilon subunit of F1F0-ATP synthase C-terminal domain [46605] (2)
10. Fe,Mn superoxide dismutase (SOD), N-terminal domain [46609] (1)
  uperfamily
  1. Fe,Mn superoxide dismutase (SOD), N-terminal domain [46610] (19)
11. Sporulation inhibitor Sda [100985] (1)
  uperfamily
  1. Sporulation inhibitor Sda [100986] (1)
12. Transcriptional repressor TraM [109631] (1)
  similar structure to L29p (scop_sf 46561); contains extra short helix; forms homodimer: an open bundle
  uperfamily
  1. Transcriptional repressor TraM [109632] (1)
13. DnaK suppressor protein DksA, alpha-hairpin domain [109635] (1)
  uperfamily
  1. DnaK suppressor protein DksA, alpha-hairpin domain [109636] (1)
14. ISY1 domain-like [140102] (1)
  uperfamily
  1. ISY1 N-terminal domain-like [140103] (1)
    N-terminal region of Pfam 06246
15. Calcyclin-binding protein-like [140106] (1)
  uperfamily
  1. Siah interacting protein N terminal domain-like [140107] (2)
    Pfam 09032
16. Endosomal sorting complex assembly domain [140111] (3)
  forms 'fan'-like heterooligomers, in which the domains of different subunit make similar interactions at the tip of the hairpin
  uperfamily
  1. VPS23 C-terminal domain [140112] (1)
  2. VPS28 N-terminal domain [140115] (1)
    includes structurally variable linker region
  3. VPS37 C-terminal domain-like [140118] (1)
    Pfam 07200; Modifier of rudimentary, Mod(r)
17. SPy1572-like [140121] (1)
  forms homodimer: an open bundle, different from the TRAM dimer
  uperfamily
  1. SPy1572-like [140122] (1)
18. Rabenosyn-5 Rab-binding domain-like [140125] (1)
  uperfamily
  1. Rabenosyn-5 Rab-binding domain-like [140126] (1)
19. MxiH-like [140129] (1)
  Type III secretion system needle
  uperfamily
  1. MxiH-like [140130] (2)
20. YnzC-like [158221] (1)
  1. YznC-like [158222] (1)
    Pfam 05979; DUF896
Type I dockerin domain [63445] (1)
tandem repeat of two calcium-binding loop-helix motifs, distinct from the EF-hand
1. Type I dockerin domain [63446] (1)
  uperfamily
  1. Type I dockerin domain [63447] (3)
LEM/SAP HeH motif [63450] (6)
helix-extended loop-helix; parallel helices
1. LEM domain [63451] (1)
  uperfamily
  1. LEM domain [63452] (2)
2. SAP domain [68906] (1)
  uperfamily
  1. SAP domain [68907] (7)
    Pfam 02037
3. Rho N-terminal domain-like [68912] (2)
  uperfamily
  1. Rho termination factor, N-terminal domain [68913] (1)
  2. YqbF C-terminal domain-like [158225] (2)
4. Recombination endonuclease VII, C-terminal and dimerization domains [68918] (1)
  uperfamily
  1. Recombination endonuclease VII, C-terminal and dimerization domains [68919] (1)
5. DNA-binding domain of EIN3-like [116768] (1)
  decorated with additional structures
  uperfamily
  1. DNA-binding domain of EIN3-like [116769] (1)
    middle part of Pfam 04873
6. PRP4-like [158230] (1)
  1. PRP4-like [158231] (1)
    Pfam 08799; pre-mRNA processing factor 4 (PRP4) like
SOCS box-like [158234] (1)
helix-loop-helix motif with orthogonally packed helices
1. SOCS box-like [158235] (1)
  1. SOCS box-like [158236] (2)
    Pfam 07525
RPB6/omega subunit-like [63561] (1)
core: 2 helices and adjacent loops
1. RPB6/omega subunit-like [63562] (2)
  the bacterial omega and eukaryotic RPB6 subunits both function in polymerase assembly; the common core is involved in conserved interactions with other subunits
  uperfamily
  1. RNA polymerase omega subunit [63563] (3)
    4 helices; irregular array
  2. RPB6 [55294] (2)
KRAB domain (Kruppel-associated box) [109639] (1)
2 helices: one short, one long; aromatic-rich iterface
1. KRAB domain (Kruppel-associated box) [109640] (1)
  uperfamily
  1. KRAB domain (Kruppel-associated box) [109641] (1)
    Pfam 01352
Cytochrome c [46625] (1)
core: 3 helices; folded leaf, opened
1. Cytochrome c [46626] (8)
  covalently-bound heme completes the core
  uperfamily
  1. monodomain cytochrome c [46627] (44)
  2. N-terminal (heme c) domain of cytochrome cd1-nitrite reductase [46671] (3)
  3. Quinoprotein alcohol dehydrogenase, C-terminal domain [68952] (2)
  4. Cytochrome bc1 domain [46676] (3)
  5. Two-domain cytochrome c [46680] (3)
    duplication: consists of two cytochrome c type domains
  6. Di-heme cytochrome c SoxA [81677] (1)
    two-domain cytochrome c with novel domain arrangement
  7. Di-heme cytochrome c peroxidase [46685] (3)
    duplication: contains two cytochrome c-type domains
  8. Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 [68956] (2)
DNA/RNA-binding 3-helical bundle [46688] (14)
core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
1. Homeodomain-like [46689] (19)
  consists only of helices
  uperfamily
  1. Homeodomain [46690] (42)
    Pfam 00046
  2. Recombinase DNA-binding domain [46728] (5)
  3. Myb/SANT domain [46739] (15)
  4. SLIDE domain [100998] (1)
    myb-related probable DNA-binding motif
  5. GARP response regulators [81683] (1)
    plant myb-related DNA-binding motif
  6. DNA-binding domain of telomeric protein [46745] (2)
    part of Pfam 00249 (Myb/SANT domain)
  7. Paired domain [46748] (3)
    duplication: consists of two domains of this fold
  8. DNA-binding domain of rap1 [46753] (1)
    duplication: consist of two domains of this fold
  9. Centromere-binding [46756] (2)
    duplication: tandem repeat of two similar domains
  10. FIS-like [100918] (4)
  11. AraC type transcriptional activator [46759] (2)
    duplication: consists of two structural repeats bipartite HTH protein
  12. Tetracyclin repressor-like, N-terminal domain [46764] (34)
  13. Middle operon regulator, Mor [109659] (1)
    contains extra N-terminal dimerisation subdomain: alpha-hairpin (27-72) dimer is a four-helical bundle with right-handed twist
  14. Psq domain [140213] (1)
    Pfam 05225
  15. Alr1493-like [140216] (1)
    Pfam 04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain (scop_cf 47405)
  16. Nanomeric phage protein-like [140219] (1)
    contains additional N and C-terminal helices and the C-terminal beta-strand forming an intersubunit beta-barrel with a channel
  17. SWIRM domain [140222] (3)
    Pfam 04433; contains extra N-terminal helix
  18. Cgl2762-like [158260] (1)
    Pfam 01527; Transposase 8
  19. RpiR-like [158263] (1)
    Pfam 01418; contains two extra helices, one at each termini; overall arrangment of five helices is similar to the helical core of the lambda integrase-like catalytic domain (scop_fa 56350)
2. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46767] (1)
  uperfamily
  1. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46768] (3)
3. ARID-like [46774] (1)
  contains extra helices at both N- and C-termini
  uperfamily
  1. ARID domain [46775] (4)
4. "Winged helix" DNA-binding domain [46785] (84)
  contains a small beta-sheet (wing)
  uperfamily
  1. Biotin repressor-like [46786] (2)
  2. LexA repressor, N-terminal DNA-binding domain [46789] (1)
  3. Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (3)
  4. Transcriptional repressor Rex, N-terminal domain [101007] (1)
  5. CAP C-terminal domain-like [46796] (9)
  6. Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4)
    Swapped dimer with the "wing" C-terminal strands
  7. ArsR-like transcriptional regulators [46801] (4)
    The N- and C-terminal helical extensions to the common fold form the dimer interface
  8. Transcriptional regulator IclR, N-terminal domain [74676] (1)
  9. MarR-like transcriptional regulators [63379] (20)
    The N- and C-terminal helical extensions to the common fold form the dimer interface
  10. DNA-binding protein Mj223 [81690] (1)
    homologous to the MarR-like family in the DNA-binding region but dimerizes differently through the N- and C-terminal helical extensions to the common fold
  11. Penicillinase repressor [101016] (4)
    homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
  12. GntR-like transcriptional regulators [46804] (4)
  13. N-terminal domain of Bacillus PurR [101021] (1)
  14. Replication terminator protein (RTP) [46807] (1)
  15. LysR-like transcriptional regulators [88979] (2)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer
  16. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46810] (1)
    contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension
  17. Transcription factor MotA, activation domain [46813] (1)
    The N- and C-terminal helical extensions to the common fold form the dimer interface (distinct from that of ArsR-like family)
  18. Transcription factor E/IIe-alpha, N-terminal domain [101024] (1)
    contains extra N-terminal helix
  19. FUR-like [101027] (1)
    contains extra N-terminal helix and an alpha+beta dimerisation subdomain
  20. Replication initiation protein [46816] (3)
    duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
  21. Helicase DNA-binding domain [46819] (5)
    follows the extended AAA-ATPase domain
  22. RecQ helicase DNA-binding domain-like [101030] (3)
    follows the tandem AAA-ATPase domain
  23. SCF ubiquitin ligase complex WHB domain [74679] (4)
  24. C-terminal fragment of elongation factor SelB [74683] (1)
  25. Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1)
  26. TnsA endonuclease, C-terminal domain [46782] (1)
  27. Plant O-methyltransferase, N-terminal domain [63475] (5)
    unknown function
  28. Linker histone H1/H5 [46827] (3)
  29. Forkhead DNA-binding domain [46832] (6)
  30. DNA-binding domain from rap30 [46841] (1)
  31. C-terminal domain of the rap74 subunit of TFIIF [63480] (1)
  32. C-terminal domain of RPA32 [46844] (1)
  33. DEP domain [63483] (5)
    membrane-binding domain
  34. Cell cycle transcription factor e2f-dp [46847] (2)
    heterodimer of two homologous chains
  35. The central core domain of TFIIE beta [46850] (1)
  36. Z-DNA binding domain [46853] (4)
    Pfam 02295
  37. P4 origin-binding domain-like [46856] (2)
    C-terminus passes through the first loop
  38. ets domain [46859] (9)
  39. Heat-shock transcription factor [46873] (2)
  40. Interferon regulatory factor [46877] (3)
    Pfam 00605
  41. 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1)
  42. Iron-dependent repressor protein [46882] (3)
  43. Dissimilatory sulfite reductase DsvD [101048] (1)
  44. La domain [101051] (3)
    Pfam 05383; RNA-binding domain
  45. Methionine aminopeptidase, insert domain [46887] (2)
    circularly permuted version of the "winged helix" fold
  46. PCI domain (PINT motif) [109671] (2)
    Pfam 01399
  47. F93-like [109674] (3)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
  48. Archaeal DNA-binding protein [109677] (1)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
  49. TrmB-like [109680] (2)
    The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families
  50. Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1)
    similar domain organization to the transcriptional regulator IclR
  51. DNA replication factor Cdt1 [109686] (1)
  52. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1)
    C-terminal part of Pfam 06272
  53. Vacuolar sorting protein domain [109692] (3)
    duplication: tandem repeat of two "winged-helix" domains
  54. Transcriptional regulator Rrf2 [109699] (2)
    Pfam 02082
  55. Rio2 serine protein kinase N-terminal domain [109702] (1)
  56. Rad21/Rec8-like [116795] (1)
    Pfam 04824
  57. Hypothetical protein PH1932 [116798] (1)
    contains new dimerisation all-alpha C-terminal subdomain
  58. An Obfc1 domain [116801] (1)
    helix-loop insertion in the HTH motif
  59. ScpB/YpuH-like [116804] (1)
    Pfam 04079
    duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain
  60. PadR-like [116807] (3)
    Pfam 03551; related to the MarR-like family (Pfam 01047)
  61. Hypothetical protein YhgG [116812] (1)
  62. ROK associated domain [140279] (3)
    found N-terminal to ROK domain in some proteins
  63. PF1790-like [140286] (1)
    sequence similarity to PH1932 in the N-terminal domain; the C-terminal domain provides new dimerisation interface made of a beta-hairpin and a coiled coil
  64. MukF N-terminal domain-like [140289] (1)
    N-terminal part of Pfam 03882
  65. CodY HTH domain [140292] (1)
    Pfam 08222
  66. FtsK C-terminal domain-like [140295] (2)
    PfamB 000224
  67. Nudix-associated domain [140299] (2)
    PfamB 002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
  68. HxlR-like [140304] (5)
    Pfam 01638; DUF24; the N- and C-terminal helical extensions to the common fold form the dimer interface similar to that of the ArsR-like family (scop_fa 46801)
  69. Marine metagenome family WH1 [158296] (1)
  70. ReutB4095-like [158299] (1)
    probable biological unit is a homohexamer
  71. PH0730 N-terminal domain-like [158302] (1)
  72. FaeA-like [158305] (1)
    Pfam 04703
  73. STY4665 C-terminal domain-like [158308] (1)
    Pfam 07515; DUF1528; the "wing" hairpin, linker between helices 1 and 2 and the C-terminal tail together form an open beta-sheet barrel
  74. PSPTO2686-like [158311] (1)
    Pfam 04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis
  75. RHA1_ro06458-like [158314] (1)
  76. YjcQ-like [158317] (1)
    Pfam 09639
  77. F112-like [158320] (1)
  78. MerB N-terminal domain-like [158323] (1)
  79. CED-4 C-terminal domain-like [158326] (1)
    similar domain architecture to AAA+ helicases
  80. ELL N2 domain-like [158329] (1)
    PfamB 026212; includes recent PDB entry 2e5n
  81. PF0610-like [158332] (1)
    PfamB 016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
  82. Rv2827c N-terminal domain-like [158335] (1)
    ~80 N-terminal residues of Pfam 09407' DUF2005
  83. Rps19E-like [158338] (1)
    Pfam 01090; local sequence similarity to members of the GntR-like family
  84. RPO3F domain-like [158341] (2)
    middle region of Pfam 05158
5. C-terminal effector domain of the bipartite response regulators [46894] (3)
  binds to DNA and RNA polymerase; the N-terminal, receiver domain belongs to the CheY family
  uperfamily
  1. PhoB-like [46895] (6)
    contains 4-stranded meander beta-sheet in the N-terminal extension
  2. GerE-like (LuxR/UhpA family of transcriptional regulators) [46900] (5)
    contains additional, fourth helix in the C-terminal extension
  3. Spo0A [46903] (2)
    elaborated with additional helices
6. TrpR-like [48295] (3)
  contains an extra shared helix after the HTH motif
  uperfamily
  1. Trp repressor, TrpR [48296] (1)
    intertwined dimer of identical 6-helical subunits
  2. Chromosomal replication initiation factor DnaA C-terminal domain IV [81695] (2)
    monomeric; contains additional N-terminal helices
  3. SPO1678-like [158345] (1)
    Pfam 06627; DUF1153
7. Ribosomal protein L11, C-terminal domain [46906] (1)
  uperfamily
  1. Ribosomal protein L11, C-terminal domain [46907] (6)
8. Ribosomal protein S18 [46911] (1)
  uperfamily
  1. Ribosomal protein S18 [46912] (2)
9. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46915] (1)
  uperfamily
  1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46916] (2)
10. N-terminal Zn binding domain of HIV integrase [46919] (1)
  uperfamily
  1. N-terminal Zn binding domain of HIV integrase [46920] (2)
    Zn-binding site is near the C-terminus
11. RNA polymerase subunit RPB10 [46924] (1)
  uperfamily
  1. RNA polymerase subunit RPB10 [46925] (2)
    Zn-binding site is near the N-terminus
12. Sigma3 and sigma4 domains of RNA polymerase sigma factors [88659] (3)
  uperfamily
  1. Sigma3 domain [88660] (3)
  2. Sigma4 domain [88665] (7)
  3. YlxM/p13-like [109706] (2)
    Pfam 04297; UPF0122
    structural and detectable sequence similarity to Sigma4 domain; contains extra C-terminal all-alpha oligomerization subdomain; forms different, helix-swapped dimers
13. KorB DNA-binding domain-like [109709] (1)
  contains HTH motif in the common core; also contains extra N-terminal helix and C-terminal subdomain of 4 helices (left-handed superhelix)
  uperfamily
  1. KorB DNA-binding domain-like [109710] (2)
    [N-terminal half of Pfam 06613]
14. Rps17e-like [116820] (1)
  uperfamily
  1. Rps17e-like [116821] (1)
    Pfam 00833
Another 3-helical bundle [81602] (5)
topologically similar to the DNA/RNA-binding bundles; distinct packing
1. FF domain [81698] (1)
  uperfamily
  1. FF domain [81699] (3)
2. Protein serine/threonine phosphatase 2C, C-terminal domain [81601] (1)
  uperfamily
  1. Protein serine/threonine phosphatase 2C, C-terminal domain [81600] (1)
3. B-form DNA mimic Ocr [101059] (1)
  uperfamily
  1. B-form DNA mimic Ocr [101060] (1)
4. DEK C-terminal domain [109715] (1)
  uperfamily
  1. DEK C-terminal domain [109716] (1)
5. IscX-like [140319] (1)
  uperfamily
  1. IscX-like [140320] (1)
    Pfam 04384; DUF528
RuvA C-terminal domain-like [46928] (9)
3 helices; bundle, right-handed twist
1. DNA helicase RuvA subunit, C-terminal domain [46929] (1)
  possibly related to UBA-like domains
  uperfamily
  1. DNA helicase RuvA subunit, C-terminal domain [46930] (3)
2. UBA-like [46934] (4)
  uperfamily
  1. UBA domain [46935] (24)
  2. TS-N domain [63423] (4)
  3. TAP-C domain-like [68973] (2)
  4. CUE domain [88995] (4)
    Pfam 02845
3. post-HMGL domain-like [89000] (2)
  uperfamily
  1. DmpG/LeuA communication domain-like [89001] (2)
  2. Conserved carboxylase domain [109725] (1)
    Pfam 02436
    duplication: contains two domains of this fold, connected with a helical linker
4. CRAL/TRIO N-terminal domain [46938] (1)
  uperfamily
  1. CRAL/TRIO N-terminal domain [46939] (3)
5. Elongation factor TFIIS domain 2 [46942] (1)
  uperfamily
  1. Elongation factor TFIIS domain 2 [46943] (1)
6. Double-stranded DNA-binding domain [46950] (1)
  uperfamily
  1. Double-stranded DNA-binding domain [46951] (2)
7. Hypothetical protein AF0491, middle domain [109728] (1)
  uperfamily
  1. Hypothetical protein AF0491, middle domain [109729] (1)
8. HBS1-like domain [109732] (1)
  possibly related to UBA-like domains
  uperfamily
  1. HBS1-like domain [109733] (1)
9. FGAM synthase PurL, linker domain [109736] (1)
  uperfamily
  1. FGAM synthase PurL, linker domain [109737] (1)
S13-like H2TH domain [81297] (1)
core: 3-4 helices
1. S13-like H2TH domain [46946] (3)
  contains a helix-two turns-helix (H2TH) motif
  uperfamily
  1. Ribosomal protein S13 [46947] (2)
    contains 3 helices and a beta-hairpin in the core and a non-globular C-terminal extension
  2. Middle domain of MutM-like DNA repair proteins [81626] (6)
    contains 4 helices in the core
  3. Topoisomerase VI-B subunit middle domain [81705] (1)
Putative DNA-binding domain [46954] (1)
core: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
1. Putative DNA-binding domain [46955] (7)
  uperfamily
  1. Domains B1 and B5 of PheRS-beta, PheT [46956] (1)
    duplication: contains two such domains related by pseudo dyad
  2. DNA repair factor XPA DNA- and RPA-binding domain, C-terminal subdomain [46959] (1)
  3. Dachshund-homology domain [74693] (2)
    Pfam 02437
  4. DNA-binding N-terminal domain of transcription activators [46962] (4)
    includes a dimerisation, antiparallel coiled-coil subdomain
  5. Terminase gpNU1 subunit domain [74696] (1)
  6. Excisionase-like [46891] (2)
    kinked C-terminal helix
  7. N-terminal subdomain of bacterial translation initiation factor IF2 [89006] (1)
Spectrin repeat-like [46965] (16)
3 helices; bundle, closed, left-handed twist; up-and-down
1. Spectrin repeat [46966] (1)
  uperfamily
  1. Spectrin repeat [46967] (5)
2. Enzyme IIa from lactose specific PTS, IIa-lac [46973] (1)
  uperfamily
  1. Enzyme IIa from lactose specific PTS, IIa-lac [46974] (1)
    form trimers with 9 helices in a bundle
3. Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain [46977] (1)
  uperfamily
  1. Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain [46978] (5)
4. Smac/diablo [46984] (1)
  uperfamily
  1. Smac/diablo [46985] (1)
5. BAG domain [63491] (1)
  uperfamily
  1. BAG domain [63492] (6)
    Pfam 02179
6. GAT-like domain [89009] (2)
  uperfamily
  1. GAT domain [89010] (3)
  2. Phosphoinositide-binding clathrin adaptor, domain 2 [100929] (2)
    this domain is associated with the N-terminal ENTH-like domain
7. Tubulin chaperone cofactor A [46988] (1)
  uperfamily
  1. Tubulin chaperone cofactor A [46989] (2)
    the C-terminal helix is shorter that the other two helices
8. Ribosomal protein S20 [46992] (1)
  uperfamily
  1. Ribosomal protein S20 [46993] (2)
9. Glycogen synthesis protein GlgS [109747] (1)
  uperfamily
  1. Glycogen synthesis protein GlgS [109748] (1)
10. Alpha-hemoglobin stabilizing protein AHSP [109751] (1)
  the bundle twist angle is close to zero (small positive value); similar to the RRF alpha-helical bundle, scop_sf 55194
  uperfamily
  1. Alpha-hemoglobin stabilizing protein AHSP [109752] (1)
11. PhoU-like [109755] (1)
  duplication: consists of two sequence each repeats adopting this fold
  uperfamily
  1. PhoU-like [109756] (4)
    Pfam 01895
12. XseB-like [116842] (1)
  helix-swapped homodimer
  uperfamily
  1. XseB-like [116843] (1)
    Pfam 02609
13. MIT domain [116846] (1)
  uperfamily
  1. MIT domain [116847] (3)
    Pfam 04212
14. PPK N-terminal domain-like [140356] (1)
  uperfamily
  1. PPK N-terminal domain-like [140357] (2)
    N-terminal part of Pfam 02503
15. MIT domain-like [140361] (1)
  uperfamily
  1. MIT domain [140362] (1)
16. Efb C-domain-like [158366] (1)
  1. Efb C-domain-like [158367] (2)
    PfamB 008033
immunoglobulin/albumin-binding domain-like [46996] (11)
3 helices; bundle, closed, left-handed twist; up-and-down; mirror topology to the spectrin-like fold
1. Bacterial immunoglobulin/albumin-binding domains [46997] (2)
  uperfamily
  1. Immunoglobulin-binding protein A modules [46998] (1)
  2. GA module, an albumin-binding domain [47001] (3)
    Pfam 01468; also includes FIVAR module, Pfam 07554
2. Plasmid maintenance system epsilon/zeta, antidote epsilon subunit [81710] (1)
  uperfamily
  1. Plasmid maintenance system epsilon/zeta, antidote epsilon subunit [81711] (1)
    dimeric
3. Families 57/38 glycoside transferase middle domain [88688] (3)
  uperfamily
  1. 4-alpha-glucanotransferase, domain 2 [89013] (1)
    family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
  2. alpha-mannosidase, domain 2 [88693] (2)
    family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
  3. AmyC C-terminal domain-like [101086] (2)
4. Phosphoprotein XD domain [101089] (1)
  uperfamily
  1. Phosphoprotein XD domain [101090] (2)
5. Staphylocoagulase [101094] (1)
  duplication: consists of two domains of this fold
  uperfamily
  1. Staphylocoagulase [101095] (1)
6. Heat shock protein 70kD (HSP70), C-terminal subdomain [100934] (1)
  uperfamily
  1. Heat shock protein 70kD (HSP70), C-terminal subdomain [100935] (3)
7. Typo IV secretion system protein TraC [101082] (1)
  uperfamily
  1. Typo IV secretion system protein TraC [101083] (1)
8. Avirulence protein AvrPto [116854] (1)
  uperfamily
  1. Avirulence protein AvrPto [116855] (1)
9. Coronavirus NSP7-like [140367] (1)
  uperfamily
  1. Coronavirus NSP7-like [140368] (1)
10. Vng1086c-like [140371] (1)
  homotetramer; comprises two dimers similar to the antidote epsilon subunit dimer
  uperfamily
  1. Vng1086c-like [140372] (1)
    Pfam 01893; UPF0058
11. AF1782-like [158372] (1)
  1. AF1782-like [158373] (2)
    Pfam 04010; DUF357
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47004] (1)
3 helices; bundle, closed, right-handed twist; up-and-down
1. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47005] (1)
  uperfamily
  1. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47006] (3)
ChaB-like [140375] (1)
3 helices, the first one is shorter than the other two; bundle, capped by a small, C-terminal beta-hairpin
1. ChaB-like [140376] (1)
  uperfamily
  1. ChaB-like [140377] (1)
    Pfam 06150
Protozoan pheromone-like [47013] (2)
3 helices; bundle, closed, left-handed twist, up-and-down
1. Protozoan pheromone proteins [47014] (1)
  uperfamily
  1. Protozoan pheromone proteins [47015] (5)
2. Hypothetical membrane protein Ta0354, soluble domain [116858] (1)
  uperfamily
  1. Hypothetical membrane protein Ta0354, soluble domain [116859] (1)
Acyl-CoA binding protein-like [47026] (2)
core: 3 helices; bundle, closed, left-handed twist; up-and-down
1. Acyl-CoA binding protein [47027] (1)
  uperfamily
  1. Acyl-CoA binding protein [47028] (2)
2. Second domain of FERM [47031] (1)
  uperfamily
  1. Second domain of FERM [47032] (9)
YqgQ-like [158378] (1)
3 helices, bundle, left-handed twist, extended overside connection between the first and second helices
1. YqgQ-like [158379] (1)
  1. YqgQ-like [158380] (1)
    Pfam 06014; DUF910
Kix domain of CBP (creb binding protein) [47039] (1)
3 helices; bundle, partly opened
1. Kix domain of CBP (creb binding protein) [47040] (1)
  uperfamily
  1. Kix domain of CBP (creb binding protein) [47041] (1)
RAP domain-like [47044] (1)
3 helices, the first one is shorter than the other two; bundle, partly opened
1. RAP domain-like [47045] (1)
  uperfamily
  1. RAP domain [47046] (1)
VHP, Villin headpiece domain [47049] (1)
3 short helices; irregular array
1. VHP, Villin headpiece domain [47050] (1)
  uperfamily
  1. VHP, Villin headpiece domain [47051] (5)
BSD domain-like [140382] (1)
core: 3 helices; triangular array; the extra N-terminal and C-terminal helices form a coiled coil structure
1. BSD domain-like [140383] (1)
  uperfamily
  1. BSD domain [140384] (2)
    Pfam 03909
TAF(II)230 TBP-binding fragment [47054] (1)
3 short helices; irregular array
1. TAF(II)230 TBP-binding fragment [47055] (1)
  uperfamily
  1. TAF(II)230 TBP-binding fragment [47056] (1)
S15/NS1 RNA-binding domain [47059] (1)
3 helices; irregular array
1. S15/NS1 RNA-binding domain [47060] (3)
  uperfamily
  1. N-terminal, RNA-binding domain of nonstructural protein NS1 [47061] (2)
  2. Ribosomal protein S15 [47064] (3)
    contains additional N-terminal helix that forms a separate unit
  3. a tRNA synthase domain [47068] (3)
Frizzled cysteine-rich domain [63500] (1)
Core: 3 helices; irregular array; disulfide-rich
1. Frizzled cysteine-rich domain [63501] (1)
  uperfamily
  1. Frizzled cysteine-rich domain [63502] (2)
T4 endonuclease V [47076] (1)
3 helices; irregular array
1. T4 endonuclease V [47077] (1)
  uperfamily
  1. T4 endonuclease V [47078] (1)
Fertilization protein [47081] (1)
core: 3 helices; bundle, closed, right-handed twist; up-and-down
1. Fertilization protein [47082] (1)
  uperfamily
  1. Fertilization protein [47083] (3)
PGBD-like [47089] (1)
core: 3 helices; bundle, closed, left-handed twist; parallel
1. PGBD-like [47090] (2)
  uperfamily
  1. Peptidoglycan binding domain, PGBD [47091] (2)
  2. MMP N-terminal domain [63427] (4)
HMG-box [47094] (1)
3 helices; irregular array
1. HMG-box [47095] (1)
  uperfamily
  1. HMG-box [47096] (12)
Histone-fold [47112] (1)
core: 3 helices; long middle helix is flanked at each end with shorter ones
1. Histone-fold [47113] (4)
  uperfamily
  1. Nucleosome core histones [47114] (23)
    form octamers composed of two copies of each of the four histones
  2. Archaeal histone [47129] (4)
  3. TBP-associated factors, TAFs [47134] (13)
  4. Bacterial histone-fold protein [101318] (2)
    duplication: two repeats of histone fold are arranged as subunits in the archael histone dimer; new structure from Thermus thermophilus (1wws) comprised of dimers similar the to the H3-H4 tetramer
Open three-helical up-and-down bundle [47143] (7)
core: 3 helices; bundle, open
1. HSC20 (HSCB), C-terminal oligomerisation domain [47144] (1)
  uperfamily
  1. HSC20 (HSCB), C-terminal oligomerisation domain [47145] (1)
2. Diol dehydratase, gamma subunit [47148] (1)
  contains irregular N-terminal subdomain
  uperfamily
  1. Diol dehydratase, gamma subunit [47149] (2)
3. Methane monooxygenase hydrolase, gamma subunit [47152] (1)
  duplication: consists of two domains of this fold
  uperfamily
  1. Methane monooxygenase hydrolase, gamma subunit [47153] (2)
4. Mitochondrial import receptor subunit Tom20 [47157] (1)
  uperfamily
  1. Mitochondrial import receptor subunit Tom20 [47158] (1)
5. Hemolysin expression modulating protein HHA [68989] (1)
  uperfamily
  1. Hemolysin expression modulating protein HHA [68990] (1)
6. EF2458-like [140404] (1)
  N-terminal helix swapped dimer; interrupted antiparallel coiled coil
  uperfamily
  1. EF2458-like [140405] (1)
    Pfam 07408; DUF1507
7. YvfG-like [158388] (1)
  1. YvfG-like [158389] (1)
    Pfam 09628
beta-catenin-interacting protein ICAT [81729] (1)
core: 3 helices; irregular array
1. beta-catenin-interacting protein ICAT [81730] (1)
  uperfamily
  1. beta-catenin-interacting protein ICAT [81731] (1)
DNA polymerase III theta subunit-like [116730] (1)
3 helices; irregular array
1. DNA polymerase III theta subunit-like [46575] (1)
  uperfamily
  1. DNA polymerase III theta subunit-like [46576] (2)
    Pfam 06440
    independent solution structure determinations of different members resulted in similar secondary structures but different folds
Four-helical up-and-down bundle [47161] (28)
core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down
1. Apolipoprotein [47162] (1)
  uperfamily
  1. Apolipoprotein [47163] (3)
    Can exist in a coiled-coil oligomeric form, see PDB entry 1AV1
    family may also include the five-helical bundle protein Apolipophorin-III
2. Aspartate receptor, ligand-binding domain [47170] (1)
  uperfamily
  1. Aspartate receptor, ligand-binding domain [47171] (2)
3. Cytochromes [47175] (2)
  Heme-containing proteins
  uperfamily
  1. Cytochrome b562 [47176] (1)
  2. Cytochrome c'-like [47179] (9)
4. Hemerythrin-like [47188] (1)
  uperfamily
  1. Hemerythrin-like [47189] (3)
    Iron-binding proteins
5. TMV-like viral coat proteins [47195] (1)
  uperfamily
  1. TMV-like viral coat proteins [47196] (3)
6. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47212] (1)
  uperfamily
  1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47213] (1)
7. Proteasome activator [47216] (1)
  uperfamily
  1. Proteasome activator [47217] (2)
8. alpha-catenin/vinculin-like [47220] (2)
  uperfamily
  1. alpha-catenin/vinculin [47221] (4)
    possible duplication: contains several domains of this fold
    The listed PDB entries contain different large fragments but not the whole proteins
  2. VBS domain [140408] (1)
    Pfam 08913; Vinculin Binding Site
9. FAT domain of focal adhesion kinase [68993] (1)
  uperfamily
  1. FAT domain of focal adhesion kinase [68994] (3)
10. Oxygen-evolving enhancer protein 3, [101112] (1)
  uperfamily
  1. Oxygen-evolving enhancer protein 3, [101113] (1)
11. Histidine-containing phosphotransfer domain, HPT domain [47226] (6)
  contains additional, fifth helix at the N-terminus
  uperfamily
  1. Aerobic respiration control sensor protein, ArcB [47227] (1)
  2. Phosphorelay protein-like [47230] (3)
  3. Chemotaxis protein CheA P1 domain [63512] (2)
  4. Sensor-like histidine kinase YojN, C-terminal domain [116868] (1)
  5. Phosphorelay protein luxU [116871] (1)
  6. SphA-like [158394] (1)
12. Bacterial GAP domain [47233] (1)
  contains extra helices in the loops at one end of the bundle
  uperfamily
  1. Bacterial GAP domain [47234] (3)
13. Outer surface protein C (OspC) [63515] (1)
  uperfamily
  1. Outer surface protein C (OspC) [63516] (1)
14. Flagellar export chaperone FliS [101116] (1)
  can form closed, open and helix-swapped bundles
  uperfamily
  1. Flagellar export chaperone FliS [101117] (2)
15. Domain of the SRP/SRP receptor G-proteins [47364] (1)
  uperfamily
  1. Domain of the SRP/SRP receptor G-proteins [47365] (7)
16. FAD-dependent thiol oxidase [69000] (1)
  uperfamily
  1. FAD-dependent thiol oxidase [69001] (2)
17. Group V grass pollen allergen [81736] (1)
  uperfamily
  1. Group V grass pollen allergen [81737] (2)
18. Nucleotidyltransferase substrate binding subunit/domain [81593] (4)
  uperfamily
  1. Family 1 bi-partite nucleotidyltransferase subunit [81740] (2)
  2. HEPN domain [89022] (2)
  3. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81592] (1)
    N-terminal catalytic domain is followed by an all-alpha domain
  4. Glutamine synthase adenylyltransferase GlnE, domain 2 [109767] (1)
19. RecG, N-terminal domain [69008] (1)
  uperfamily
  1. RecG, N-terminal domain [69009] (1)
20. Colicin D immunity protein [101125] (1)
  uperfamily
  1. Colicin D immunity protein [101126] (1)
21. Nickel-containing superoxide dismutase, NiSOD [109770] (1)
  uperfamily
  1. Nickel-containing superoxide dismutase, NiSOD [109771] (2)
22. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109775] (1)
  contains extra alpha+beta subdomain formed by the N- and C-termini.
  uperfamily
  1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109776] (1)
23. Domain from hypothetical 2610208m17rik protein [109779] (1)
  uperfamily
  1. Domain from hypothetical 2610208m17rik protein [109780] (1)
24. TrmE connector domain [116878] (1)
  uperfamily
  1. TrmE connector domain [116879] (1)
25. YppE-like [140415] (1)
  flattened bundle at one end with helices 2 and coming in contact and separating helices 1 and 3
  uperfamily
  1. YppE-like [140416] (3)
    Pfam 08807; DUF1798
26. MW0975(SA0943)-like [140423] (1)
  open bundle; there is a long groove between helices 1 and 4
  uperfamily
  1. MW0975(SA0943)-like [140424] (1)
27. VPS28 C-terminal domain-like [140427] (1)
  uperfamily
  1. VPS28 C-terminal domain-like [140428] (1)
    C-terminal part of Pfam 03997
28. TM1646-like [158397] (1)
  1. TM1646-like [158398] (1)
    Pfam 03885; DUF327
PTS-regulatory domain, PRD [63519] (1)
core: 4 helices; bundle, closed, right-handed twist; 1 crossover connection
1. PTS-regulatory domain, PRD [63520] (1)
  duplication: consists of two domains of this fold
  uperfamily
  1. PTS-regulatory domain, PRD [63521] (1)
Ferritin-like [47239] (6)
core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
1. Ferritin-like [47240] (9)
  contains bimetal-ion centre in the middle of the bundle
  uperfamily
  1. Ferritin [47241] (34)
  2. Ribonucleotide reductase-like [47253] (18)
  3. Manganese catalase (T-catalase) [100951] (2)
  4. YciF-like [140445] (2)
    Pfam 05974; DUF892
  5. half-ferritin [140450] (1)
    comprise of alpha-hairpin subunits forming the ferritin-like four-helical bundle; assembles further in a homodecamer
  6. PMT1231-like [158402] (1)
    PfamB 016165
  7. MiaE-like [158405] (1)
    Pfam 06175; tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
  8. AMB4284-like [158408] (1)
    possible rubrerythrin
  9. Rv2844-like [158411] (1)
    PfamB 061364
2. Cobalamin adenosyltransferase-like [89028] (2)
  crossover loop goes across a different side of the 4-helical bundle; no internal metal-binding site
  uperfamily
  1. Cobalamin adenosyltransferase [89032] (2)
  2. Hypothetical protein Ta1238 [89029] (1)
3. EsxAB dimer-like [140453] (1)
  (hetero)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
  uperfamily
  1. ESAT-6 like [140454] (2)
    Pfam 06013; the conserwed WxG motif makes the turn at the alpha-hairpin tip
4. PE/PPE dimer-like [140459] (2)
  (hetero)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals inside the bundle
  uperfamily
  1. PE [140460] (1)
    Pfam 00934; pairs with with the N-terminal hairpin of PPE
  2. PPE [140463] (1)
    Pfam 00823; contains extra C-terminal alpha-hairpin, unlike the PE family subunit
5. HP0062-like [158414] (1)
  (homo)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
  1. HP0062-like [158415] (1)
    Pfam 09647
6. SO2669-like [158418] (1)
  (homo)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
  1. SO2669-like [158419] (1)
4-helical cytokines [47265] (1)
core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
1. 4-helical cytokines [47266] (3)
  there are two different topoisomers of this fold with different entanglements of the two crossover connections
  uperfamily
  1. Long-chain cytokines [47267] (14)
  2. Short-chain cytokines [47286] (14)
  3. Interferons/interleukin-10 (IL-10) [47305] (13)
    contains an additional helix in one of the crossover connections
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47322] (1)
core: 4 helices; bundle; one loop crosses over one side of the bundle
1. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47323] (1)
  uperfamily
  1. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47324] (10)
Acyl carrier protein-like [47335] (3)
4 helices, bundle; helix 3 is shorter than others; up-and-down
1. ACP-like [47336] (3)
  uperfamily
  1. Acyl-carrier protein (ACP) [47337] (9)
  2. Peptidyl carrier domain [47342] (1)
  3. apo-D-alanyl carrier protein [63535] (1)
2. Colicin E immunity proteins [47345] (1)
  uperfamily
  1. Colicin E immunity proteins [47346] (3)
3. Retrovirus capsid dimerization domain-like [47353] (2)
  uperfamily
  1. Retrovirus capsid protein C-terminal domain [47354] (4)
  2. SCAN domain [140466] (2)
    Pfam 02023; forms segment-swapped dimers compared to the retroviral capsid domain
Bromodomain-like [47363] (15)
4 helices; bundle; minor mirror variant of up-and-down topology
1. Bromodomain [47370] (1)
  uperfamily
  1. Bromodomain [47371] (5)
2. alpha-ketoacid dehydrogenase kinase, N-terminal domain [69012] (1)
  uperfamily
  1. alpha-ketoacid dehydrogenase kinase, N-terminal domain [69013] (3)
3. Acyl-CoA dehydrogenase C-terminal domain-like [47203] (2)
  multidomain flavoprotein; N-terminal domain is all-alpha; the middle domain is open (5,8) barrel
  uperfamily
  1. Medium chain acyl-CoA dehydrogenase-like, C-terminal domain [47204] (12)
  2. acyl-CoA oxidase C-terminal domains [74714] (2)
    duplication: tandem repeat of this fold
4. Plant invertase/pectin methylesterase inhibitor [101148] (1)
  contains a short alpha-hairpin at the N-terminal extension
  uperfamily
  1. Plant invertase/pectin methylesterase inhibitor [101149] (2)
    Pfam 04043
5. Mob1/phocein [101152] (1)
  common fold is elaborated with additional short helices; contains a zinc-binding site
  uperfamily
  1. Mob1/phocein [101153] (2)
6. Bacteriocin immunity protein-like [109797] (2)
  uperfamily
  1. Carnobacteriocin B2 immunity protein [109798] (1)
  2. EntA-Im [140475] (1)
7. LemA-like [140478] (1)
  helices 2 and 3 are shorther than helices 1 and 4
  uperfamily
  1. LemA-like [140479] (1)
    Pfam 04011
8. MAST3 pre-PK domain-like [140482] (1)
  this domain precedes the Protein Kinase domain in Microtubule-associated serine/threonine-protein kinase 3 (MAST3)
  uperfamily
  1. MAST3 pre-PK domain-like [140483] (1)
9. PA2201 N-terminal domain-like [140486] (1)
  uperfamily
  1. PA2201 N-terminal domain-like [140487] (1)
    trimerisation domain
10. Nqo1C-terminal domain-like [140490] (1)
  contains extra C-terminal helix that caps the bundle at one end and Fe4-S4 cluster at the other end
  uperfamily
  1. Nqo1C-terminal domain-like [140491] (1)
    PfamB 000336; sequence similarity to the Fe4-S4 ferredoxins in the cluser-binding site
11. Bacillus cereus metalloprotein-like [158430] (1)
  Duplication: tandem repeat of two domains of this fold with similar sequences; binds a dimetal ion cluster between the repeats
  1. Bacillus cereus metalloprotein-like [158431] (2)
12. Ta0600-like [158436] (1)
  1. Ta0600-like [158437] (2)
    Pfam 03685; UPF0147
13. DsbB-like [158442] (1)
  contains an extra helix in a long loop between helices 3 and 4
  1. DsbB-like [158443] (1)
    Pfam 02600
14. IVS-encoded protein-like [158446] (1)
  IVS: Intervening sequence with conserved ORF in eubacterial 23S rRNA genes; forms a homopentamer with a toroid-shaped structure containing a tapered central channel
  1. IVS-encoded protein-like [158447] (2)
    Pfam 05635
15. YqcC-like [158452] (1)
  1. YqcC-like [158453] (1)
    Pfam 04287; DUF446
ROP-like [47379] (8)
4 helices; dimer of identical alpha-hairpin subunits; bundle, closed, left-handed twist
1. ROP protein [47380] (1)
  uperfamily
  1. ROP protein [47381] (1)
2. Homodimeric domain of signal transducing histidine kinase [47384] (1)
  uperfamily
  1. Homodimeric domain of signal transducing histidine kinase [47385] (3)
3. Nonstructural protein ns2, Nep, M1-binding domain [101156] (1)
  uperfamily
  1. Nonstructural protein ns2, Nep, M1-binding domain [101157] (1)
4. Dimerisation domain of CENP-B [101160] (1)
  uperfamily
  1. Dimerisation domain of CENP-B [101161] (1)
5. Hypothetical protein D-63 [109801] (1)
  uperfamily
  1. Hypothetical protein D-63 [109802] (1)
6. HP1531-like [140496] (1)
  contains short extra helix in the loop between the two bundle-forming helices
  uperfamily
  1. HP1531-like [140497] (1)
    Small sequence family, specific to Helicobacteraceae
7. BAS1536-like [140500] (1)
  uperfamily
  1. BAS1536-like [140501] (2)
    PfamB 015565
8. FHV B2 protein-like [140506] (1)
  uperfamily
  1. FHV B2 protein-like [140507] (1)
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47390] (1)
4 helices; bundle, closed, right-handed twist
1. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47391] (1)
  dimer of identical alpha-hairpin motifs
  uperfamily
  1. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47392] (2)
Orange domain-like [158456] (1)
4 helices; dimer of identical alpha-hairpin subunits;
1. Orange domain-like [158457] (1)
  1. Hairy Orange domain [158458] (1)
    Pfam 07527
Soluble domain of poliovirus core protein 3a [89042] (1)
4 helices; bundle, closed, right-handed twist
1. Soluble domain of poliovirus core protein 3a [89043] (1)
  dimer of identical alpha-hairpin motifs
  uperfamily
  1. Soluble domain of poliovirus core protein 3a [89044] (1)
Transcription factor IIA (TFIIA), alpha-helical domain [47395] (1)
4 helices; bundle, closed, right-handed twist
1. Transcription factor IIA (TFIIA), alpha-helical domain [47396] (1)
  dimer of non-identical alpha-hairpins
  uperfamily
  1. Transcription factor IIA (TFIIA), alpha-helical domain [47397] (4)
    heterodimer of two homologous chains
Ectatomin subunits [47400] (1)
4 helices; bundle, closed, left-handed twist
1. Ectatomin subunits [47401] (1)
  disulfide-linked heterodimer of similar alpha-hairpin subunits
  uperfamily
  1. Ectatomin subunits [47402] (2)
Dimerisation interlock [47405] (4)
4 helices; bundle, closed, right-handed twist
1. SinR repressor dimerisation domain-like [47406] (1)
  intertwined heterodimer of two homologous chains
  uperfamily
  1. SinR repressor dimerisation domain-like [47407] (2)
2. Dimerization cofactor of HNF-1 alpha [100957] (1)
  uperfamily
  1. Dimerization cofactor of HNF-1 alpha [100958] (1)
3. Docking domain A of the erythromycin polyketide synthase (DEBS) [101166] (1)
  uperfamily
  1. Docking domain A of the erythromycin polyketide synthase (DEBS) [101167] (1)
4. Phenylalanine zipper [109805] (1)
  interlocking dimer with longer helices and aromatic-rich core
  uperfamily
  1. Adapter protein APS, dimerisation domain [109806] (1)
lambda repressor-like DNA-binding domains [47412] (1)
core: 4 helices; folded leaf, closed
1. lambda repressor-like DNA-binding domains [47413] (13)
  uperfamily
  1. POU-specific domain [47414] (3)
  2. Phage repressors [47419] (7)
    consists of different sequence families of HTH repressors of phage origins
  3. SinR domain-like [47432] (8)
  4. Cyanase N-terminal domain [47435] (1)
    probably does not bind to DNA
  5. GalR/LacI-like bacterial regulator [47438] (4)
    lacks the first helix of canonical fold
    3 helices; bundle, partly opened, right-handed twist
  6. YdiL-like [109813] (2)
    contains extra C-terminal all-alpha dimerization subdomain; the dimer may bind DNA
  7. CUT domain [116891] (4)
    Pfam 02376
  8. Probable transcriptional regulator VC1968, N-terminal domain [116898] (1)
  9. Bacteriophage CII protein [140520] (1)
    Pfam 05269; a compact helix-swapped dimer of the canonical fold; includes the extra C-terminal teramerisation region (alpha-helix); in the tetramer-DNA complex only two of the four HTH motifs interact with DNA
  10. NE0471 C-terminal domain-like [140523] (1)
  11. PrgX N-terminal domain-like [140526] (1)
    Part of Pfam 01381
  12. EDF1-like [140529] (1)
    part of Pfam 01381
  13. NE1354 [140532] (2)
    contains extra C-terminal dimerisation arm (beta-strand)
Signal peptide-binding domain [47445] (1)
4 helices; orthogonal array
1. Signal peptide-binding domain [47446] (1)
  uperfamily
  1. Signal peptide-binding domain [47447] (4)
A DNA-binding domain in eukaryotic transcription factors [47453] (1)
4 helices; the long C-terminal helix protrudes from the domain and binds to DNA
1. A DNA-binding domain in eukaryotic transcription factors [47454] (1)
  uperfamily
  1. A DNA-binding domain in eukaryotic transcription factors [47455] (2)
HLH-like [47458] (2)
4-helices; bundle, closed, left-handed twist; 2 crossover connections
1. HLH, helix-loop-helix DNA-binding domain [47459] (1)
  dimer of two identical helix-loop-helix subunits
  uperfamily
  1. HLH, helix-loop-helix DNA-binding domain [47460] (9)
2. Docking domain B of the erythromycin polyketide synthase (DEBS) [101173] (1)
  uperfamily
  1. Docking domain B of the erythromycin polyketide synthase (DEBS) [101174] (1)
HAMP domain-like [158471] (1)
dimer of helix-loop-helix segments; distict from the HLH-like fold; parallel four-helical bundle with two overside connections
1. HAMP domain-like [158472] (1)
  1. HAMP domain [158473] (1)
    Pfam 00672
EF Hand-like [47472] (4)
core: 4 helices; array of 2 hairpins, opened
1. EF-hand [47473] (11)
  Duplication: consists of two EF-hand units: each is made of two helices connected with calcium-binding loop
  uperfamily
  1. Calbindin D9K [47474] (2)
    made of two EF-hands only
  2. S100 proteins [47478] (17)
    dimer: subunits are made of two EF-hands
  3. Polcalcin [89048] (3)
    calcium-binding pollen allergen; two EF-hands per subunit
  4. Osteonectin [47489] (1)
    5 helices; two EF-hands plus one of additional helices in the N-terminal part
  5. Parvalbumin [47492] (9)
    6-helices; array of 3 hairpins, closed
    made with two-helical hairpin and two EF-hands
  6. Calmodulin-like [47502] (49)
    Duplication: made with two pairs of EF-hands
  7. Eps15 homology domain (EH domain) [47543] (4)
  8. Cbp40 (plasmodial specific CaII-binding protein LAV1-2) [81758] (1)
    4 EF-hands assembled in a compact structure like the Penta-EF-hand proteins; contains additional N-terminal all-alpha subdomain
  9. Penta-EF-hand proteins [63550] (11)
  10. EF-hand modules in multidomain proteins [47547] (8)
  11. p25-alpha [140538] (2)
    Pfam 05517; comprises two degenerate EF-hands and extra C-terminal helix, packed agains the bundle end
2. Insect pheromone/odorant-binding proteins [47565] (1)
  the N-terminal extension, containing a few short helices, forms a flexible lid for the binding cavity
  uperfamily
  1. Insect pheromone/odorant-binding proteins [47566] (6)
3. Hypothetical protein MTH865 [69025] (1)
  uperfamily
  1. Hypothetical protein MTH865 [69026] (1)
4. Cloroperoxidase [47571] (1)
  duplication: consists of 2 similar domains composed of 2 EF hand-like motifs each
  uperfamily
  1. Cloroperoxidase [47572] (1)
CH domain-like [47575] (3)
core: 4 helices: bundle
1. Calponin-homology domain, CH-domain [47576] (1)
  uperfamily
  1. Calponin-homology domain, CH-domain [47577] (12)
    Pfam 00307
2. X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain [81761] (1)
  uperfamily
  1. X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain [81762] (1)
3. Hook domain [116907] (1)
  uperfamily
  1. Hook domain [116908] (1)
    N-terminal part of Pfam 05622
Domain of poly(ADP-ribose) polymerase [47586] (1)
core: 4 helices: bundle; unusual topology
1. Domain of poly(ADP-ribose) polymerase [47587] (1)
  duplication: consists of 2 helix-loop-helix structural repeats
  uperfamily
  1. Domain of poly(ADP-ribose) polymerase [47588] (3)
SWIB/MDM2 domain [47591] (1)
core: 4 helices: open bundle; capped by two small 3-stranded beta-sheets
duplication: consists of two structural repeats
1. SWIB/MDM2 domain [47592] (1)
  binds to the transactivation domain of human p53
  uperfamily
  1. SWIB/MDM2 domain [47593] (5)
    Pfam 02201
Pre-protein crosslinking domain of SecA [81766] (1)
core: 4 helices: bundle; flanked by two short beta-hairpins
duplication: consists of two structural repeats
1. Pre-protein crosslinking domain of SecA [81767] (1)
  uperfamily
  1. Pre-protein crosslinking domain of SecA [81768] (2)
Ribbon-helix-helix [47597] (1)
core: 4 helices; array of 2 hairpins, opened
1. Ribbon-helix-helix [47598] (11)
  formerly Met repressor-like; dimeric proteins; the N-termini form a small beta-sheet ribbon
  uperfamily
  1. Arc/Mnt-like phage repressors [47599] (2)
  2. CopG-like [100970] (5)
    similar to the phage repressor family
  3. Omega transcriptional repressor [100971] (1)
    plasmid-encoded, similar to the phage repressor family
  4. Met repressor, MetJ (MetR) [100972] (1)
  5. NE0241-like [140544] (1)
    contains extra C-terminal long helix; currently consists of an orphan protein
  6. SeqA N-terminal domain-like [140547] (1)
    N-terminal part of Pfam 03925
  7. Trafficking protein A-like [140550] (1)
  8. VCA0319-like [140553] (1)
    COG4453; extended and extra C-terminal helices; potential component of the bi-partite system also including an acetyltransferase
  9. VirC2-like [158482] (1)
    Pfam 07181; duplicated ribbon-helix-helix motif; fold forms a trefoil knot
  10. PutA pre-N-terminal region-like [158485] (1)
    in PutA it forms a separate ribbon-helix-helix domain connected to the N-terminal enzymatic domain by a flexible linker
  11. MJ0366-like [158488] (1)
    PfamB 022101; duplicated ribbon-helix-helix motif; forms trefoil knot; predicted DNA binding
GST C-terminal domain-like [47615] (1)
core: 4 helices; bundle, closed, left-handed twist; right-handed superhelix
1. GST C-terminal domain-like [47616] (2)
  this domains follows the thioredoxin-like N-terminal domain
  uperfamily
  1. Glutathione S-transferase (GST), C-terminal domain [47617] (44)
  2. Arc1p N-terminal domain-like [158491] (1)
    PfamB 021108
Methionine synthase domain-like [47643] (3)
4 helices; bundle, left-handed twist; right-handed superhelix
1. Methionine synthase domain [47644] (1)
  uperfamily
  1. Methionine synthase domain [47645] (1)
2. Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain [47648] (1)
  uperfamily
  1. Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain [47649] (6)
3. TM0693-like [140560] (1)
  helix-swapped dimer; in which the two last helices of this fold form a single coiled-coil helix
  uperfamily
  1. TM0693-like [140561] (1)
KaiA/RbsU domain [101214] (1)
4 helices; bundle, right-handed twist; right-handed superhelix
1. KaiA/RbsU domain [101215] (2)
  uperfamily
  1. Circadian clock protein KaiA, C-terminal domain [101216] (3)
  2. Phosphoserine phosphatase RsbU, N-terminal domain [109836] (1)
    forms a helix-swapped dimer that otherwise is similar to the KaiA domain dimer
STAT-like [47654] (6)
4 long helices; bundle, left-handed twist (coiled coil); right-handed superhelix
1. STAT [47655] (1)
  uperfamily
  1. STAT [47656] (3)
2. t-snare proteins [47661] (1)
  uperfamily
  1. t-snare proteins [47662] (6)
3. Cag-Z [109839] (1)
  four-helical bundle without significant twist
  uperfamily
  1. Cag-Z [109840] (1)
4. CAPPD, an extracellular domain of amyloid beta A4 protein [109843] (1)
  the first three helices are longer than the fourth one and, taken separately, adopt a Spectrin repeat-like fold (scop_cf 46965)
  uperfamily
  1. CAPPD, an extracellular domain of amyloid beta A4 protein [109844] (1)
5. FlgN-like [140566] (1)
  the last helix is shorter than the three others; a short extra helix between helices 2 an 3 fills the gap in the bundle
  uperfamily
  1. FlgN-like [140567] (1)
    Pfam 05130
6. MukF C-terminal domain-like [140570] (1)
  uperfamily
  1. MukF C-terminal domain-like [140571] (1)
    C-terminal part of Pfam 03882
N-cbl like [47667] (5)
4 helices; bundle, left-handed twist; left-handed superhelix
1. N-terminal domain of cbl (N-cbl) [47668] (1)
  uperfamily
  1. N-terminal domain of cbl (N-cbl) [47669] (1)
2. Transferrin receptor-like dimerisation domain [47672] (1)
  uperfamily
  1. Transferrin receptor-like dimerisation domain [47673] (2)
3. Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [47676] (1)
  uperfamily
  1. Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [47677] (2)
    Smart 00509
4. HIV integrase-binding domain [140576] (1)
  uperfamily
  1. HIV integrase-binding domain [140577] (1)
    N-terminal part of PfamB 012949
5. PG0775 C-terminal domain-like [158494] (1)
  1. PG0775 C-terminal domain-like [158495] (1)
    PfamB 133436
Replisome organizer (g39p helicase loader/inhibitor protein) [89063] (1)
4 helices; bundle, right-handed twist; left-handed superhelix
1. Replisome organizer (g39p helicase loader/inhibitor protein) [89064] (1)
  uperfamily
  1. Replisome organizer (g39p helicase loader/inhibitor protein) [89065] (1)
Hypothetical protein YqbG [116914] (1)
core: 4 helices; bundle, right-handed twist; left-handed superhelix
1. Hypothetical protein YqbG [116915] (1)
  uperfamily
  1. Hypothetical protein YqbG [116916] (1)
DnaD domain-like [158498] (1)
4 helices; bundle, right-handed twist; left-handed superhelix
1. DnaD domain-like [158499] (1)
  1. DnaD domain [158500] (1)
    Pfam 04271
C-terminal domain of B transposition protein [47680] (1)
4 helices; irregular array
1. C-terminal domain of B transposition protein [47681] (1)
  uperfamily
  1. C-terminal domain of B transposition protein [47682] (1)
HAND domain of the nucleosome remodeling ATPase ISWI [101223] (1)
4 helices; irregular array
1. HAND domain of the nucleosome remodeling ATPase ISWI [101224] (1)
  uperfamily
  1. HAND domain of the nucleosome remodeling ATPase ISWI [101225] (1)
N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89068] (1)
4 helices; irregular array
1. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89069] (1)
  uperfamily
  1. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89070] (1)
Anaphylotoxins (complement system) [47685] (1)
4 helices; irregular array, disulfide-linked
1. Anaphylotoxins (complement system) [47686] (1)
  uperfamily
  1. Anaphylotoxins (complement system) [47687] (2)
    can be classified as disulfide-rich
Cytochrome c oxidase subunit h [47693] (1)
4 helices; irregular array, disulfide-linked
1. Cytochrome c oxidase subunit h [47694] (1)
  uperfamily
  1. Cytochrome c oxidase subunit h [47695] (1)
Crustacean CHH/MIH/GIH neurohormone [81777] (1)
4 helices; irregular array, disulfide-linked
1. Crustacean CHH/MIH/GIH neurohormone [81778] (1)
  uperfamily
  1. Crustacean CHH/MIH/GIH neurohormone [81779] (1)
C-terminal domain of DFF45/ICAD (DFF-C domain) [81782] (1)
4 helices; folded leaf; right-handed superhelix
1. C-terminal domain of DFF45/ICAD (DFF-C domain) [81783] (1)
  uperfamily
  1. C-terminal domain of DFF45/ICAD (DFF-C domain) [81784] (1)
BH2638-like [158503] (1)
4 helices, folded leaf, right-handed superhelix; some similarity to the DFF-C domain fold (scop_cf 81782)
1. BH2638-like [158504] (1)
  1. BH2638-like [158505] (1)
    Pfam 05256; UPF0223
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin [47698] (1)
4 helices; folded leaf; right-handed superhelix
1. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin [47699] (3)
  can be classified as disulfide-rich
  uperfamily
  1. Plant lipid-transfer and hydrophobic proteins [47700] (7)
  2. Proteinase/alpha-amylase inhibitors [47708] (3)
  3. Seed storage protein, 2S albumin [47715] (3)
    two chains result from a single-chain precursor
p53 tetramerization domain [47718] (1)
core: 4 helices; bundle
1. p53 tetramerization domain [47719] (1)
  homotetramer
  uperfamily
  1. p53 tetramerization domain [47720] (1)
Bcr-Abl oncoprotein oligomerization domain [69035] (1)
core: 4 long helices; bundle
1. Bcr-Abl oncoprotein oligomerization domain [69036] (1)
  homotetramer
  uperfamily
  1. Bcr-Abl oncoprotein oligomerization domain [69037] (1)
Domain of early E2A DNA-binding protein, ADDBP [47723] (1)
4 helices; bundle, partly opened
1. Domain of early E2A DNA-binding protein, ADDBP [47724] (1)
  this domain is the first in the fragment of known structure
  uperfamily
  1. Domain of early E2A DNA-binding protein, ADDBP [47725] (1)
IHF-like DNA-binding proteins [47728] (1)
core: 4 helices; bundle, partly opened, capped with a beta-sheet
1. IHF-like DNA-binding proteins [47729] (2)
  dimer of identical subunits
  uperfamily
  1. Prokaryotic DNA-bending protein [47730] (8)
  2. DNA-binding domain (fragment?) of the TraM protein [63566] (1)
    old provisional classification awaiting the entire protein structure; structure of a different fragment of this protein (PDB 2g7o) is classified into a different superfamily
TraM-like [140580] (1)
multihelical oligomeric protein; structure of whole subunit is not known; the N-terminal part is implicated in DNA binding, the middle region forms tetrameric parallel coiled coil, surrounded by the C-terminal helices
1. TraM-like [140581] (1)
  uperfamily
  1. TraM-like [140582] (2)
    Pfam 05261
CO dehydrogenase ISP C-domain like [47740] (1)
core: 4 helices, bundle
1. CO dehydrogenase ISP C-domain like [47741] (1)
  contains 2Fe-2S cluster
  uperfamily
  1. CO dehydrogenase ISP C-domain like [47742] (8)
Protein HNS-dependent expression A; HdeA [47751] (1)
4 helices; the three last helices form a bundle similar to that of the RuvA C-domain
1. Protein HNS-dependent expression A; HdeA [47752] (1)
  overall fold is similar to the fold of N-terminal subdomain of the GluRS anticodon-binding domain (1GLN)
  uperfamily
  1. Protein HNS-dependent expression A; HdeA [47753] (1)
PABP domain-like [63569] (2)
4 helices; an orthogonal array
1. PABC (PABP) domain [63570] (1)
  uperfamily
  1. PABC (PABP) domain [63571] (4)
2. Ribosomal protein L20 [74731] (1)
  uperfamily
  1. Ribosomal protein L20 [74732] (4)
Chemotaxis receptor methyltransferase CheR, N-terminal domain [47756] (1)
4 helices; an orthogonal array
1. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47757] (1)
  uperfamily
  1. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47758] (1)
Dcp2 domain-like [140585] (1)
4 helices; orthogonal array of two alpha hairpins
1. Dcp2 domain-like [140586] (1)
  uperfamily
  1. Dcp2 box A domain [140587] (1)
    Pfam 05026
Type III secretion system domain [140590] (1)
core: 4 helices, orthogonal array; right-handed superhelix
1. Type III secretion system domain [140591] (3)
  uperfamily
  1. TyeA-like [140592] (1)
    Pfam 09059
  2. YopR Core [140595] (1)
    Pfam 09025, contains extra N-terminal helix
  3. LcrE-like [140598] (1)
    Duplication; contains two domains of this fold; Pfam 07201 (HrpJ-like) covers the first domain and the N-terminal half of the second domain
YugE-like [116921] (1)
4-helices; bundle; right-handed twist
1. YugE-like [116922] (1)
  uperfamily
  1. YugE-like [116923] (1)
PWI domain [101232] (1)
4 helices; up-and-down bundle; topological similarity to the bromodomain-like and SAM domain-like folds
1. PWI domain [101233] (1)
  uperfamily
  1. PWI domain [101234] (1)
PAH2 domain [47761] (1)
4 helices; open up-and-down bundle; binds alpha-helical peptides
1. PAH2 domain [47762] (1)
  uperfamily
  1. PAH2 domain [47763] (2)
Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81789] (1)
4 helices; open up-and-down bundle; flexible N-terminal tail
1. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81790] (1)
  uperfamily
  1. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81791] (1)
XPC-binding domain [101237] (1)
4 helices; array
1. XPC-binding domain [101238] (1)
  uperfamily
  1. XPC-binding domain [101239] (3)
DinB/YfiT-like putative metalloenzymes [109853] (1)
core: 4 helices; bundle, closed, left-handed twist; an unusual topology with a higher contact order
1. DinB/YfiT-like putative metalloenzymes [109854] (4)
  contains metal-binding site on the bundle surface surrounded by loops
  uperfamily
  1. YfiT-like putative metal-dependent hydrolases [109855] (1)
    probably distantly related to the DinB family (Pfam 05163)
  2. DinB-like [140603] (4)
    Pfam 05163
  3. Sden0562-like [158519] (1)
    Pfam 09351; DUF1993
  4. Maleylpyruvate isomerase-like [158522] (1)
EspA/CesA-like [116926] (1)
4 helices; bundle, closed, left ight-handed twist; interlocked (hetero)dimer of 2-helical subunits
1. EspA/CesA-like [116927] (2)
  secreted protein and its chaperone both adopt similar substructures in the heterodimer
  uperfamily
  1. EspA-like [116928] (1)
    Pfam 03433
  2. EspA chaperone CesA [116931] (1)
NblA-like [109858] (1)
4 helices; dimer of identical alpha-hairpin subunits; open bundle
1. NblA-like [109859] (1)
  uperfamily
  1. NblA-like [109860] (1)
    Pfam 04485
EF2947-like [140606] (1)
4 helices; "diamond" array; duplication: N-terminal and C-terminal pairs of helices are related by pseudo dyad
1. EF2947-like [140607] (1)
  uperfamily
  1. EF2947-like [140608] (1)
EB1 dimerisation domain-like [140611] (1)
dimeric 4-helical bundle with a coiled coil at one end formed by the longer N-terminal helices
1. EB1 dimerisation domain-like [140612] (1)
  uperfamily
  1. EB1 dimerisation domain-like [140613] (1)
    Pfam 03271
SAM domain-like [47768] (16)
4-5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins
1. SAM/Pointed domain [47769] (3)
  uperfamily
  1. Pointed domain [47770] (7)
  2. SAM (sterile alpha motif) domain [47773] (16)
  3. Variant SAM domain [158526] (2)
    shares a sequence motif with Pfam 07647, but has a distinct packing of helices
2. RuvA domain 2-like [47781] (7)
  duplication: contains two helix-hairpin-helix (HhH) motifs
  uperfamily
  1. DNA helicase RuvA subunit, middle domain [47782] (3)
  2. Excinuclease UvrC C-terminal domain [81795] (1)
  3. NAD+-dependent DNA ligase, domain 3 [47786] (1)
  4. Topoisomerase V repeat domain [140626] (1)
  5. Hef domain-like [140629] (4)
    helicase/nuclease domain; forms homo and heterodimers; probably includes the Excinuclease UvrC C-terminal domain (scop_fa 81795, that contains a single NMR structure of a monomeric truncated domain, 1kft)
  6. Tex HhH-containing domain-like [158531] (1)
    tandem repeat of two Ruva_2-like domains
  7. ComEA-like [158534] (2)
    sequence similarity to the HhH-motif domains of the PsbU-like and Tex-like families
3. C-terminal domain of RNA polymerase alpha subunit [47789] (1)
  contains one classic and one pseudo HhH motifs
  uperfamily
  1. C-terminal domain of RNA polymerase alpha subunit [47790] (3)
4. Rad51 N-terminal domain-like [47794] (3)
  contains one classic and one pseudo HhH motifs
  uperfamily
  1. DNA repair protein Rad51, N-terminal domain [47795] (4)
  2. NusA extra C-terminal domains [109873] (1)
  3. Hypothetical protein AF1548, C-terminal domain [116936] (1)
5. Barrier-to-autointegration factor, BAF [47798] (1)
  contains one classic and one pseudo HhH motifs
  uperfamily
  1. Barrier-to-autointegration factor, BAF [47799] (1)
6. DNA polymerase beta, N-terminal domain-like [47802] (1)
  contains one classic and one pseudo HhH motifs
  uperfamily
  1. DNA polymerase beta, N-terminal domain-like [47803] (4)
7. PsbU/PolX domain-like [81585] (2)
  contains one classic and one pseudo HhH motifs
  uperfamily
  1. DNA polymerase beta-like, second domain [81584] (4)
    topological similarity to the N-terminal domain
  2. PsbU-like [158539] (1)
    Pfam 06514
8. 5' to 3' exonuclease, C-terminal subdomain [47807] (1)
  uperfamily
  1. 5' to 3' exonuclease, C-terminal subdomain [47808] (8)
9. HRDC-like [47819] (4)
  uperfamily
  1. HRDC domain from helicases [47820] (3)
  2. RNA polymerase II subunit RBP4 (RpoF) [69044] (3)
  3. RNase D C-terminal domains [140643] (1)
    tandem repeat of two domains of this fold, the first domain belongs to Pfam 00570
  4. EXOSC10 HRDC domain-like [140646] (2)
10. lambda integrase-like, N-terminal domain [47823] (1)
  uperfamily
  1. lambda integrase-like, N-terminal domain [47824] (3)
11. Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain [47831] (1)
  uperfamily
  1. Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain [47832] (1)
12. Hypothetical protein YjbJ [69047] (1)
  uperfamily
  1. Hypothetical protein YjbJ [69048] (1)
13. Putative methyltransferase TM0872, insert domain [81799] (1)
  uperfamily
  1. Putative methyltransferase TM0872, insert domain [81800] (2)
14. eIF2alpha middle domain-like [116742] (1)
  uperfamily
  1. eIF2alpha middle domain-like [116743] (3)
15. YozE-like [140652] (1)
  uperfamily
  1. YozE-like [140653] (2)
    Pfam 06855; DUF1250
16. GspK insert domain-like [158544] (1)
  tandem repeat of two SAM-like domains iserted into pilin fold; domain 1 contains one classic HhH motif
  1. GspK insert domain-like [158545] (1)
    middle part of Pfam 03934
Retroviral matrix proteins [47835] (1)
4-5 helices; right-handed superhelix
1. Retroviral matrix proteins [47836] (6)
  the 5th, C-terminal helix is missing in some of the member structures
  uperfamily
  1. Immunodeficiency virus matrix proteins [47837] (2)
  2. HTLV-II matrix protein [47842] (1)
    the C-terminal helix region is disordered(?)
  3. Mason-Pfizer monkey virus matrix protein [47845] (1)
    the C-terminal helix region is missing(?)
  4. GAG polyprotein M-domain [47848] (1)
    the C-terminal helix region is missing(?)
  5. EIAV matrix antigen [69051] (1)
  6. MMLV matrix protein-like [81803] (2)
Flavivirus capsid protein C [101256] (1)
core: 5 helices; right-handed superhelix; swapped dimer with the two long C-terminal helices
1. Flavivirus capsid protein C [101257] (1)
  uperfamily
  1. Flavivirus capsid protein C [101258] (2)
Hepatitis B viral capsid (hbcag) [47851] (1)
5 helices; array; two long helices form a hairpin that dimerizes into a 4-helical bundle
1. Hepatitis B viral capsid (hbcag) [47852] (1)
  uperfamily
  1. Hepatitis B viral capsid (hbcag) [47853] (1)
Apolipophorin-III [47856] (1)
5 helices; bundle, closed, left-handed twist
1. Apolipophorin-III [47857] (1)
  uperfamily
  1. Apolipophorin-III [47858] (2)
Methenyltetrahydrofolate cyclohydrolase-like [101261] (1)
5 helices; bundle, closed, left-handed twist
1. Methenyltetrahydrofolate cyclohydrolase-like [101262] (1)
  uperfamily
  1. Methenyltetrahydrofolate cyclohydrolase-like [101263] (1)
    COG3404
A middle domain of Talin 1 [109879] (1)
5 helices; bundle, closed, left-handed twist; helices 2-5 adopt the Four-helical up-and-down bundle fold (scop_cf 47161)
1. A middle domain of Talin 1 [109880] (1)
  uperfamily
  1. A middle domain of Talin 1 [109881] (1)
I/LWEQ domain [109884] (1)
5 helices; bundle, closed, left-handed twist
1. I/LWEQ domain [109885] (1)
  uperfamily
  1. I/LWEQ domain [109886] (2)
    Pfam 01608
    actin-binding motif that adopts different folds; possibly refolds upon binding
RNA-binding protein She2p [116941] (1)
5 helices; bundle, closed, left-handed twist; topological similarity to the middle domain of the L-aspartase-like fold (scop_cf 48556)
1. RNA-binding protein She2p [116942] (1)
  uperfamily
  1. RNA-binding protein She2p [116943] (1)
Hyaluronidase domain-like [140656] (3)
5 helices; bundle, closed, left-handed twist; up-and-down (meander) topology
1. Hyaluronidase post-catalytic domain-like [140657] (1)
  uperfamily
  1. Hyaluronidase post-catalytic domain-like [140658] (2)
2. TTHA0068-like [140663] (1)
  uperfamily
  1. TTHA0068-like [140664] (2)
    Pfam 03745; DUF309
3. FLJ32549 domain-like [158548] (1)
  1. FLJ32549 domain-like [158549] (1)
    middle part of Pfam 09404; DUF2003
YoaC-like [140669] (1)
5 helices; bundle, one crossover connection, the arrangement of the first four helices is similar to the KaiA/RbsU domain fold (scop_cf 101214)
1. YoaC-like [140670] (1)
  uperfamily
  1. YoaC-like [140671] (1)
Saposin-like [47861] (2)
5 helices; folded leaf, closed
1. Saposin [47862] (4)
  Lipid-binding can promote conformational changes and oligomerisation in some members
  uperfamily
  1. Saposin B [81806] (1)
    the alternative subunit conformation is an open four-helical bundle; helices 3 and 4 form a contiguous helix
  2. NKL-like [47863] (3)
  3. Ameobapore A [101266] (1)
  4. Swaposin [47866] (1)
    circularly permuted saposin domain inserted in plant acid proteases
2. Bacteriocin AS-48 [47869] (1)
  uperfamily
  1. Bacteriocin AS-48 [47870] (1)
Annexin [47873] (1)
5 helices; folded leaf, closed
1. Annexin [47874] (1)
  duplication: consists of four domains of the same fold
  uperfamily
  1. Annexin [47875] (14)
TAFH domain-like [158552] (1)
5 helices; folded leaf, closed
1. TAFH domain-like [158553] (1)
  1. TAFH domain-like [158554] (2)
    Pfam 07531
Transducin (alpha subunit), insertion domain [47894] (1)
5 helices; folded leaf
1. Transducin (alpha subunit), insertion domain [47895] (1)
  this domain interrupts the G-protein common fold
  uperfamily
  1. Transducin (alpha subunit), insertion domain [47896] (4)
Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47911] (1)
5 helices; irregular array; left-handed superhelix
1. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47912] (1)
  uperfamily
  1. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47913] (1)
Left-handed superhelix [47916] (4)
core: 4-5 helices; bundle; left-handed superhelix
1. C-terminal domain of alpha and beta subunits of F1 ATP synthase [47917] (1)
  uperfamily
  1. C-terminal domain of alpha and beta subunits of F1 ATP synthase [47918] (8)
2. Ypt/Rab-GAP domain of gyp1p [47923] (1)
  uperfamily
  1. Ypt/Rab-GAP domain of gyp1p [47924] (1)
    duplication: contains two similar domains of this fold
3. 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain [69055] (1)
  uperfamily
  1. 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain [69056] (2)
4. BH3980-like [158560] (1)
  1. BH3980-like [158561] (3)
    Pfam 06304; DUF1048
ATPD N-terminal domain-like [47927] (2)
core: 5 helices; bundle
1. N-terminal domain of the delta subunit of the F1F0-ATP synthase [47928] (1)
  uperfamily
  1. N-terminal domain of the delta subunit of the F1F0-ATP synthase [47929] (1)
2. AF1862-like [158568] (1)
  probable biological unit is a hexamer
  1. Cas Cmr5-like [158569] (1)
    Pfam 09701; CRISPR-associated protein
ERP29 C domain-like [47932] (2)
5 helices; bundle
1. ERP29 C domain-like [47933] (1)
  uperfamily
  1. ERP29 C domain-like [47934] (2)
2. Helical domain of Sec23/24 [81811] (1)
  uperfamily
  1. Helical domain of Sec23/24 [81812] (2)
Functional domain of the splicing factor Prp18 [47937] (1)
core: 5 helices; bundle
1. Functional domain of the splicing factor Prp18 [47938] (1)
  uperfamily
  1. Functional domain of the splicing factor Prp18 [47939] (1)
Retrovirus capsid protein, N-terminal core domain [47942] (1)
core: 5 helices; bundle
1. Retrovirus capsid protein, N-terminal core domain [47943] (1)
  uperfamily
  1. Retrovirus capsid protein, N-terminal core domain [47944] (5)
GINS helical bundle-like [158572] (1)
5 helices, staggered bundle;
1. GINS helical bundle-like [158573] (4)
  common to all subunits of the GINS complex
  1. PSF1 N-terminal domain-like [158574] (1)
  2. PSF2 C-terminal domain-like [158577] (1)
    C-terminal part of PF04128
  3. PSF3 C-terminal domain-like [158580] (1)
    C-terminal part of Pfam 06425
  4. SLD5 N-terminal domain-like [158583] (1)
    N-terminal part of Pfam 05916
Jann4075-like [158586] (1)
core: 5 helices; the C-terminal helix is surrounded by the others; similarity to some EF-hand domains
1. Jann4075-like [158587] (1)
  1. Jann4075-like [158588] (1)
Cyclin-like [47953] (1)
core: 5 helices; one helix is surrounded by the others
1. Cyclin-like [47954] (3)
  duplication: consists of two domains of this fold
  uperfamily
  1. Cyclin [47955] (11)
  2. Transcription factor IIB (TFIIB), core domain [47965] (2)
  3. Retinoblastoma tumor suppressor domains [47969] (1)
Arp2/3 complex 21 kDa subunit ARPC3 [69059] (1)
5 helices; one helix is surrounded by the others
1. Arp2/3 complex 21 kDa subunit ARPC3 [69060] (1)
  uperfamily
  1. Arp2/3 complex 21 kDa subunit ARPC3 [69061] (1)
RNase III domain-like [69064] (1)
core: 5 helices; one helix is surrounded by the others
1. RNase III domain-like [69065] (2)
  uperfamily
  1. RNase III catalytic domain-like [69066] (3)
    Pfam 00636
  2. PF0609-like [140675] (1)
    specific to Thermococci; shares conserved carboxylic residues and similar dimerisation mode with the RNase III domain; contains integrated in the fold extra C-terminal helix, making it similar to the core fold of Ribosomal protein S7 (scop_cf 47972)
Ribosomal protein S7 [47972] (1)
core: 5 helices; contains one more helix and a beta-hairpin outside the core
1. Ribosomal protein S7 [47973] (1)
  uperfamily
  1. Ribosomal protein S7 [47974] (4)
post-AAA+ oligomerization domain-like [48018] (1)
core: 5 helices: bundle
1. post-AAA+ oligomerization domain-like [48019] (2)
  associated with N-terminal domain from the AAA+ family of P-loop hydrolases
  uperfamily
  1. DNA polymerase III clamp loader subunits, C-terminal domain [48020] (10)
    contains an extra helix
  2. MgsA/YrvN C-terminal domain-like [158600] (3)
PAP/OAS1 substrate-binding domain [81632] (1)
core: 5-helical bundle; up-and-down; right-handed twist
1. PAP/OAS1 substrate-binding domain [81631] (5)
  this domain follows the catalytic nucleotidyltransferase domain
  uperfamily
  1. Poly(A) polymerase, PAP, middle domain [81630] (2)
  2. 2'-5'-oligoadenylate synthetase 1, OAS1, second domain [101271] (1)
  3. Archaeal tRNA CCA-adding enzyme substrate-binding domain [101274] (1)
  4. RNA editing terminal uridyl transferase 2, RET2, domain 2 [140679] (1)
  5. AadK C-terminal domain-like [158607] (1)
    C-terminal part of Pfam 04439; Streptomycin adenylyltransferase; contains extra C-terminal helix
Anti-sigma factor AsiA [69069] (1)
core: 5 helices: orthogonal array
1. Anti-sigma factor AsiA [69070] (1)
  uperfamily
  1. Anti-sigma factor AsiA [69071] (1)
Antibiotic binding domain of TipA-like multidrug resistance regulators [89081] (1)
5 helices: orthogonal array
1. Antibiotic binding domain of TipA-like multidrug resistance regulators [89082] (1)
  uperfamily
  1. Antibiotic binding domain of TipA-like multidrug resistance regulators [89083] (1)
Surp module (SWAP domain) [109904] (1)
5 helices: irregular array
1. Surp module (SWAP domain) [109905] (1)
  uperfamily
  1. Surp module (SWAP domain) [109906] (3)
    Pfam 01805
YgfY-like [109909] (1)
5 helices; array; forms a tight dimer in crystals
1. YgfY-like [109910] (1)
  uperfamily
  1. YgfY-like [109911] (1)
    Pfam 03937; despite the Pfam annotation, this family shows no topological similarity to the TPR repeat proteins
Hypothetical protein YhaI [109914] (1)
core: 5 helices; orthogonal array; folding similarity to the TipA-S domain (1ny9)
1. Hypothetical protein YhaI [109915] (1)
  oligomerizes via extra N-terminal helix forming trimeric coil-coiled
  uperfamily
  1. Hypothetical protein YhaI [109916] (1)
Hypothetical protein At3g22680 [109919] (1)
5 helices; array; probable biological unit is a homodimer
1. Hypothetical protein At3g22680 [109920] (1)
  uperfamily
  1. Hypothetical protein At3g22680 [109921] (1)
SP0561-like [140682] (1)
5 helices; array; includes extra N-terminal and C-terminal short strands forming parrallel beta-sheet ladder
1. SP0561-like [140683] (1)
  uperfamily
  1. SP0561-like [140684] (1)
    Pfam 08984; DUF1858
RbcX-like [158614] (1)
5 helices per subunit; irregular array of short and long helices; swapping of the C-terminal helices in the dimer
1. RbcX-like [158615] (1)
  1. RbcX-like [158616] (3)
    Pfam 02341 (note typo in the Pfam name: RcbX)
YheA-like [158621] (1)
5 helices; "kinked" antiparallel coiled coil; forms flexible oligomeric assemblies via two different dimerisation interfaces
1. YheA/YmcA-like [158622] (2)
  1. YmcA-like [158623] (1)
    N-terminal and C-terminal parts correspond to PfamB 012831 and PfamB 007043, respectively
  2. YheA-like [158626] (3)
    Pfam 06133; DUF964
RPA2825-like [158633] (1)
5 helices, array; long flexible loop between helices 1 and 2; the remaining helices are arranged similar to the PGBD-like fold (scop_cf 47089)
1. RPA2825-like [158634] (1)
  1. RPA2825-like [158635] (1)
    PfamB 041910
ENT-like [158638] (1)
5 helices, irregular array, right-handed superhelix
1. ENT-like [158639] (1)
  1. Emsy N terminal (ENT) domain-like [158640] (1)
    Pfam 03735
YfmB-like [140687] (1)
5 helices, array; buried N-terminal helix; some topological similarity (circular permutation?) to the Nucleotidyltransferase substrate binding subunit/domain (scop_sf 81593)
1. YfmB-like [140688] (1)
  uperfamily
  1. YfmB-like [140689] (1)
N-terminal domain of adenylylcyclase associated protein, CAP [101277] (1)
6 helices: bundle; left-handed twist, up-and-down topology
1. N-terminal domain of adenylylcyclase associated protein, CAP [101278] (1)
  uperfamily
  1. N-terminal domain of adenylylcyclase associated protein, CAP [101279] (1)
IpaD-like [140692] (1)
6 helices; bundle, up-and-down; can be divided into two four-helical bundles sharing two helices (3 and 6), which are twice longer than the rest
1. IpaD-like [140693] (1)
  uperfamily
  1. IpaD-like [140694] (2)
    Pfam 06511
Iron-dependent repressor protein, dimerization domain [47978] (1)
6 helices, homodimer of 3-helical domains
1. Iron-dependent repressor protein, dimerization domain [47979] (1)
  uperfamily
  1. Iron-dependent repressor protein, dimerization domain [47980] (3)
Glutamyl tRNA-reductase dimerization domain [69074] (1)
6 helices, homodimer of 3-helical domains
1. Glutamyl tRNA-reductase dimerization domain [69075] (1)
  uperfamily
  1. Glutamyl tRNA-reductase dimerization domain [69076] (1)
GRIP domain [101282] (1)
6 helices, homodimer of 3-helical domains
1. GRIP domain [101283] (1)
  uperfamily
  1. GRIP domain [101284] (1)
BAR/IMD domain-like [116747] (1)
6 helices, homodimer of 3-helical domains
1. BAR/IMD domain-like [103657] (4)
  core: dimeric six-helical bundle; protuding long helices form aniparallel coiled coils at both bundle ends
  uperfamily
  1. BAR domain [103658] (5)
    sensor of membrane curvature
  2. Arfaptin, Rac-binding fragment [64599] (1)
  3. IMD domain [140703] (1)
    Pfam 08397
  4. FCH domain [158645] (2)
    Pfam 00611; Fes/CIP4 homology domain
L27 domain [101287] (1)
6 helices, heterodimer of 3-helical domains
1. L27 domain [101288] (1)
  uperfamily
  1. L27 domain [101289] (9)
Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109924] (1)
dimer of 3-helical segments; consists of two subdomains: 4-helical bundle and coiled coil
1. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109925] (1)
  uperfamily
  1. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109926] (1)
Phage replication organizer domain [140712] (1)
6 helices, homodimer of 3-helical domains
1. Phage replication organizer domain [140713] (1)
  DNA binding induces further oligomerization
  uperfamily
  1. Phage replication organizer domain [140714] (1)
    Pfam 06720
YejL-like [158650] (1)
6 helices; intertwined homodimer of three-helical subunits, bundle
1. YejL-like [158651] (1)
  1. YejL-like [158652] (5)
    Pfam 07208; DUF1414
Mediator hinge subcomplex-like [140717] (1)
6 helices; heterodimer of structurally similar subunits; the N-terminal hairpins form a four-helical bundle, whereas the C-terminal helices form coiled coil structure
1. Mediator hinge subcomplex-like [140718] (2)
  uperfamily
  1. CSE2-like [140719] (1)
    Pfam 07544
  2. MED7 hinge region [140722] (1)
    C-terminal part of Pfam 05983
DEATH domain [47985] (1)
6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
1. DEATH domain [47986] (4)
  uperfamily
  1. DEATH domain, DD [81312] (9)
    Pfam 00531
  2. DEATH effector domain, DED [81388] (2)
  3. Caspase recruitment domain, CARD [81313] (5)
  4. Pyrin domain, PYD [101298] (2)
GntR ligand-binding domain-like [48007] (1)
core: 6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
1. GntR ligand-binding domain-like [48008] (1)
  uperfamily
  1. GntR ligand-binding domain-like [48009] (2)
AF0941-like [140725] (1)
6 helices, arranged into two interconnected 3-helical bundles; can also be described as a 'kinked' four-helical bundle; right-handed superhelix
1. AF0941-like [140726] (1)
  uperfamily
  1. AF0941-like [140727] (1)
NusB-like [48012] (1)
6 helices: bundle; one central helix is surrounded by 5 others
1. NusB-like [48013] (3)
  uperfamily
  1. Antitermination factor NusB [48014] (3)
  2. Hypothetical protein MG027 [101303] (1)
  3. RmsB N-terminal domain-like [109930] (1)
YutG-like [101306] (1)
core: 6 helices; bundle; one central helix is surrounded by 5 others
1. YutG-like [101307] (1)
  uperfamily
  1. YutG-like [101308] (3)
    Pfam 01892; DUF64
N-terminal domain of DnaB helicase [48023] (1)
6 helices: array
1. N-terminal domain of DnaB helicase [48024] (1)
  uperfamily
  1. N-terminal domain of DnaB helicase [48025] (1)
Invasion protein A (SipA) , C-terminal actin binding domain [101311] (1)
6 helices: orthogonal array
1. Invasion protein A (SipA) , C-terminal actin binding domain [101312] (1)
  uperfamily
  1. Invasion protein A (SipA) , C-terminal actin binding domain [101313] (1)
MtlR-like [158667] (1)
multihelical; 8-helical up-and-down bundle
1. MtlR-like [158668] (1)
  1. MtlR-like [158669] (2)
    Pfam 05068; mannitol repressor
Guanido kinase N-terminal domain [48033] (1)
irregular array of 6 short helices
1. Guanido kinase N-terminal domain [48034] (1)
  uperfamily
  1. Guanido kinase N-terminal domain [48035] (8)
Scaffolding protein gpD of bacteriophage procapsid [48044] (1)
core: 6 helices; one central helix is surrounded by 5 others
1. Scaffolding protein gpD of bacteriophage procapsid [48045] (1)
  uperfamily
  1. Scaffolding protein gpD of bacteriophage procapsid [48046] (1)
Hemocyanin, N-terminal domain [48049] (1)
6 helices; bundle; one central helix is surrounded by 5 others
1. Hemocyanin, N-terminal domain [48050] (1)
  uperfamily
  1. Hemocyanin, N-terminal domain [48051] (2)
Sama2622-like [158674] (1)
core: 6 helices; bundle; one central helix is surrounded by 5 others
1. Sama2622-like [158675] (1)
  1. Sama2622-like [158676] (1)
Di-copper centre-containing domain [48055] (1)
multihelical
1. Di-copper centre-containing domain [48056] (2)
  duplication: contains two structural repeats
  uperfamily
  1. Hemocyanin middle domain [48057] (4)
  2. Catechol oxidase [48061] (1)
DBL homology domain (DH-domain) [48064] (1)
multihelical; core: 5-helical bundle
1. DBL homology domain (DH-domain) [48065] (1)
  uperfamily
  1. DBL homology domain (DH-domain) [48066] (10)
    Pfam 00621
LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48075] (1)
multihelical; contains compact array of 6 short helices
1. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48076] (1)
  uperfamily
  1. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48077] (1)
RuBisCo LSMT C-terminal, substrate-binding domain [81821] (1)
multihelical; irregular array of long and short helices
1. RuBisCo LSMT C-terminal, substrate-binding domain [81822] (1)
  uperfamily
  1. RuBisCo LSMT C-terminal, substrate-binding domain [81823] (1)
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48080] (1)
multihelical bundle; contains buried central helix
1. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48081] (1)
  uperfamily
  1. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48082] (6)
    C-terminal domain is all-alpha
YcfC-like [101321] (1)
multihelical; contains two buried central helices
1. YcfC-like [101322] (1)
  uperfamily
  1. YcfC-like [101323] (1)
    Pfam 04356; DUF489
PA2201 C-terminal domain-like [140730] (1)
multihelical; seven-helical bundle with buried central helix
1. PA2201 C-terminal domain-like [140731] (1)
  uperfamily
  1. PA2201 C-terminal domain-like [140732] (1)
Rv1873-like [140735] (1)
multihelical; contains unusually short buried central helix
1. Rv1873-like [140736] (1)
  uperfamily
  1. Rv1873-like [140737] (1)
    contains conserved motif HWuW at the beginning of the central helix
RUN domain-like [140740] (1)
multihelical; 3-helical bundle similar to one half of the DEATH domain fold is flanked by two alpha-hairpins forming a four-helical bundle; the axes of the three-helical and four-helical bundles are aproximately orthogonal to each other
1. RUN domain-like [140741] (1)
  uperfamily
  1. RUN domain [140742] (1)
    Pfam 02759
SipA N-terminal domain-like [140745] (1)
multihelical; bundle; the last helix is buried inside the bundle
1. SipA N-terminal domain-like [140746] (1)
  uperfamily
  1. SipA N-terminal domain-like [140747] (1)
    N-terminal part of Pfam 09052
Transcription factor STAT-4 N-domain [48091] (1)
multihelical; can be divided into two subdomains
1. Transcription factor STAT-4 N-domain [48092] (1)
  uperfamily
  1. Transcription factor STAT-4 N-domain [48093] (1)
TerB-like [158681] (1)
multihelical; contains two central helices; duplication: there are two three-helical repeats related by pseudo twofold symmetry
1. TerB-like [158682] (2)
  members of this superfamily probably related to the tellurite resistance protein TerB (Pfam 05099) of yet undetermined structure
  1. COG3793-like [158683] (1)
    Pfam 07049; DUF1332
  2. PG1108-like [158686] (1)
Regulator of G-protein signaling, RGS [48096] (1)
multihelical; consists of two all-alpha subdomains
contains a 4-helical bundle with left-handed twist and up-and-down topology
1. Regulator of G-protein signaling, RGS [48097] (1)
  uperfamily
  1. Regulator of G-protein signaling, RGS [48098] (9)
SopE-like GEF domain [81831] (1)
multihelical; consists of two all-alpha subdomains each containing a 3-helical bundle with right-handed twist
1. SopE-like GEF domain [81832] (1)
  uperfamily
  1. SopE-like GEF domain [81833] (3)
    C-terminal part of Pfam 05364
Variable surface antigen VlsE [74747] (1)
multihelical; consists of two all-alpha subdomains; contains a 4-helical bundle with left-handed twist and up-and-down topology
1. Variable surface antigen VlsE [74748] (1)
  uperfamily
  1. Variable surface antigen VlsE [74749] (1)
YgfB-like [101326] (1)
multihelical; consists of two tightly associated 3-helical bundles with different twists
1. YgfB-like [101327] (1)
  uperfamily
  1. YgfB-like [101328] (1)
Hypothetical protein MTH393 [101331] (1)
multihelical; consists of two all-alpha subdomains; dimer
1. Hypothetical protein MTH393 [101332] (1)
  uperfamily
  1. Hypothetical protein MTH393 [101333] (1)
PG0816-like [140752] (1)
multihelical; comprises two helical bundles, both are topologically similar to the RuvA C-terminal domain-like fold (scop_cf 46928)
1. PG0816-like [140753] (1)
  uperfamily
  1. PG0816-like [140754] (1)
    Pfam 08989; DUF1896
UraD-like [158693] (1)
multihelical; irregular array of long and short helices
1. UraD-Like [158694] (1)
  1. UraD-like [158695] (3)
    Pfam 09349; OHCU decarboxylase (formerly DUF1991)
Sec63 N-terminal domain-like [158701] (1)
multihelical; consists of two helical subdomains
1. Sec63 N-terminal domain-like [158702] (2)
  1. Sec63 N-terminal domain [158703] (1)
    N-terminal part of Pfam 02889
  2. Achaeal helicase C-terminal domain [158706] (1)
Carbamoyl phosphate synthetase, large subunit connection domain [48107] (1)
multihelical; consists of two all-alpha subdomains
possible duplication: subdomains have similar topologies
1. Carbamoyl phosphate synthetase, large subunit connection domain [48108] (1)
  uperfamily
  1. Carbamoyl phosphate synthetase, large subunit connection domain [48109] (1)
Heme-dependent peroxidases [48112] (1)
multihelical; consists of two all-alpha domains
1. Heme-dependent peroxidases [48113] (3)
  uperfamily
  1. CCP-like [48114] (14)
  2. Catalase-peroxidase KatG [74753] (4)
    duplication: tandem repeat of two CCP-like domains
  3. Myeloperoxidase-like [48132] (4)
Ribosomal protein L19 (L19e) [48139] (1)
multihelical; consists of two different 3-helical domains connected by a long, partly helical linker
1. Ribosomal protein L19 (L19e) [48140] (1)
  uperfamily
  1. Ribosomal protein L19 (L19e) [48141] (1)
PSPTO4464-like [158709] (1)
multihelical; consists of two subdomains at the ends of a long connecting helix
1. PSPTO4464-like [158710] (1)
  1. PSPTO4464-like [158711] (1)
    Pfam 04751; DUF615
GatB/YqeY motif [89094] (1)
multihelical; consists of two different alpha-helical bundles (4-helical and 3-helical)
1. GatB/YqeY motif [89095] (2)
  uperfamily
  1. GatB/YqeY domain [89096] (1)
  2. GatB/GatE C-terminal domain-like [140757] (3)
    assigned to the same Pfam 02637 family as YeqY by the presence of a common sequence motif with an alpha-hairpin structure
YfbU-like [116959] (1)
multihelical; consist of two subdomains; forms 24-mer with the N-terminal sudbomains packing around the 4-fold axis and the C-terminal domains interacting at the 2-fold and 3-fold axes
1. YfbU-like [116960] (1)
  uperfamily
  1. YfbU-like [116961] (1)
    Pfam 03887
MG296-like [158714] (1)
multihelical; in crystal forms helical polymers by swapping the two N-terminal helices to the next subunit in polymer; three subunits per turn of polymer helix
1. MG296-like [158715] (1)
  1. MG296-like [158716] (1)
    Pfam 09644
Hypothetical protein MPN330 [116964] (1)
multihelical; consists of three different 4-helical bundles
1. Hypothetical protein MPN330 [116965] (1)
  uperfamily
  1. Hypothetical protein MPN330 [116966] (1)
HD-domain/PDEase-like [109603] (1)
multihelical; consists of two different alpha-helical bundles
1. HD-domain/PDEase-like [109604] (5)
  uperfamily
  1. HD domain [101340] (13)
    Pfam 01966; metal dependent phosphohydrolases
  2. PDEase [48548] (6)
    Pfam 00233; multihelical; can be divided into three subdomains
  3. modified HD domain [116973] (1)
    retains the superfamily core fold but lacks the conserved metal-binding site
  4. MioX-like [140769] (2)
    Pfam 05153; DUF706
  5. Ppx associated domain [140773] (1)
    this domain is C-terminal to Ppx domain in some Exopolyphosphatases
Superantigen MAM [101343] (1)
multihelical; consists of two different alpha-helical bundles
1. Superantigen MAM [101344] (1)
  uperfamily
  1. Superantigen MAM [101345] (1)
Influenza virus matrix protein M1 [48144] (1)
multihelical; consists of two different all-alpha subdomains, 4 helices each
1. Influenza virus matrix protein M1 [48145] (1)
  superficially similar to membrane translocation domains
  uperfamily
  1. Influenza virus matrix protein M1 [48146] (1)
DNA-glycosylase [48149] (1)
multihelical; consists of two all-alpha domains
1. DNA-glycosylase [48150] (6)
  uperfamily
  1. Endonuclease III [48151] (1)
  2. Mismatch glycosylase [48154] (4)
  3. 3-Methyladenine DNA glycosylase I (Tag) [74756] (1)
  4. 3-Methyladenine DNA glycosylase III (MagIII) [101349] (1)
  5. DNA repair glycosylase, 2 C-terminal domains [48157] (2)
  6. AgoG-like [116976] (2)
An anticodon-binding domain of class I aminoacyl-tRNA synthetases [48162] (1)
multihelical; consists of two all-alpha domains
1. An anticodon-binding domain of class I aminoacyl-tRNA synthetases [48163] (2)
  uperfamily
  1. C-terminal domain of glutamyl-tRNA synthetase (GluRS) [48164] (1)
  2. C-terminal domain of class I lysyl-tRNA synthetase [74759] (1)
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101352] (1)
multihelical; consists of two all-alpha subdomains
1. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101353] (1)
  uperfamily
  1. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101354] (1)
R1 subunit of ribonucleotide reductase, N-terminal domain [48167] (1)
multihelical consists of two all-alpha subdomains
subdomain 1 (residues 10-100) is a 4-helical bundle
1. R1 subunit of ribonucleotide reductase, N-terminal domain [48168] (1)
  uperfamily
  1. R1 subunit of ribonucleotide reductase, N-terminal domain [48169] (2)
BEACH domain [81836] (1)
multihelical, complex architecture
1. BEACH domain [81837] (1)
  uperfamily
  1. BEACH domain [81838] (2)
    Pfam 02138
Cryptochrome/photolyase FAD-binding domain [48172] (1)
multihelical; consists of two all-alpha subdomains
1. Cryptochrome/photolyase FAD-binding domain [48173] (1)
  uperfamily
  1. Cryptochrome/photolyase FAD-binding domain [48174] (5)
6-phosphogluconate dehydrogenase C-terminal domain-like [48178] (1)
multihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold symmetry
1. 6-phosphogluconate dehydrogenase C-terminal domain-like [48179] (12)
  N-terminal domain is Rossmann-fold with a family-specific C-terminal extension
  uperfamily
  1. Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain [48180] (5)
    Hydroxyisobutyrate dehydrogenase domain is similar to one structural repeat in the 6-phosphogluconate dehydrogenase domain
  2. Mannitol 2-dehydrogenase [81843] (1)
  3. Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) [48184] (2)
  4. HCDH C-domain-like [48187] (3)
  5. Conserved hypothetical protein MTH1747 [74762] (1)
  6. UDP-glucose/GDP-mannose dehydrogenase dimerisation domain [48191] (2)
  7. N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [48194] (1)
  8. Glycerol-3-phosphate dehydrogenase [48197] (2)
  9. Ketopantoate reductase PanE [69084] (1)
  10. ProC C-terminal domain-like [116984] (3)
    similar dimer to the class I KARI
  11. HMD dimerization domain-like [140777] (1)
    dimer similar to those of the GDP-mannose 6-dehydrogenase and class I KARI domains
  12. TyrA dimerization domain-like [140780] (3)
    new dimerisation mode with swapping of C-terminal helices
Uteroglobin-like [48200] (1)
multihelical
1. Uteroglobin-like [48201] (1)
  disulfide-linked dimer of two identical chains, 4 helices in each
  uperfamily
  1. Uteroglobin-like [48202] (4)
alpha/alpha toroid [48207] (6)
multihelical; up to seven alpha-hairpins are arranged in closed circular array; there may be sequence similarities between different superfamilies
1. Six-hairpin glycosidases [48208] (9)
  uperfamily
  1. Glucoamylase [48209] (2)
  2. Cellulases catalytic domain [48213] (13)
  3. N-acylglucosamine (NAG) epimerase [48222] (2)
  4. Glycosyltransferase family 36 C-terminal domain [63588] (2)
    overall domain organization is similar to Bacterial glucoamylase
  5. Bacterial glucoamylase C-terminal domain-like [81850] (2)
    overall domain organization is similar to Lactobacillus maltose phosphorylase
  6. Hypothetical protein YteR [89108] (1)
    unknown function; weak sequence similarity to the catalytic domain of cellulases
  7. Glycosyl Hydrolase Family 88 [109953] (1)
    Pfam 07470
  8. CPF0428-like [158737] (2)
    Pfam 06824; DUF1237
  9. Trehalase-like [158742] (1)
    Pham 01204
2. Seven-hairpin glycosidases [48225] (1)
  uperfamily
  1. Class I alpha-1;2-mannosidase, catalytic domain [48226] (5)
3. Chondroitin AC/alginate lyase [48230] (2)
  incomplete toroid
  uperfamily
  1. Alginate lyase A1-III [48231] (1)
  2. Hyaluronate lyase-like catalytic, N-terminal domain [48234] (6)
4. Family 10 polysaccharide lyase [81853] (1)
  uperfamily
  1. Family 10 polysaccharide lyase [81854] (2)
    incomplete toroid made of four hairpins
5. Terpenoid cyclases/Protein prenyltransferases [48239] (4)
  uperfamily
  1. Terpenoid cyclase N-terminal domain [48240] (2)
    incomplete toroid made of four hairpins
  2. Terpene synthases [48243] (2)
    consists of two toroid domains: one of six and one of five hairpins
  3. Protein prenyltransferases [48246] (3)
  4. Complement components [48251] (3)
    probably related to other families, but has no known enzymatic activity
6. LanC-like [158745] (1)
  comprises seven hairpins
  1. LanC-like [158746] (1)
    Pfam 05147; there are seven internal sequence repeats
Citrate synthase [48255] (1)
multihelical; consists of two all-alpha domains
1. Citrate synthase [48256] (1)
  uperfamily
  1. Citrate synthase [48257] (7)
    duplication: large domain consists of two structural repeats
    the second repeat is interrupted by the small domain
Cytochrome P450 [48263] (1)
multihelical
1. Cytochrome P450 [48264] (1)
  uperfamily
  1. Cytochrome P450 [48265] (23)
Flagellar transcriptional activator FlhD [63591] (1)
multihelical; forms intertwined dimer of identical 5-helical subunits
1. Flagellar transcriptional activator FlhD [63592] (1)
  uperfamily
  1. Flagellar transcriptional activator FlhD [63593] (1)
    contains an HTH motif
HP0242-like [158751] (1)
multihelical; intertwined homodimer of four-helical subunits, forming catenated triangular ring-like structures; pseudo knot
1. HP0242-like [158752] (1)
  1. HP0242-like [158753] (1)
    Pfam 09442; DUF2018
SMc04008-like [158756] (1)
multihelcal; intertwined homodimer; there are 4 core helices in each subunits; contains putative metal ion-binding motif MxxxxxCxxC in the conserved surface site
1. SMc04008-like [158757] (1)
  1. SMc04008-like [158758] (1)
    Pfam 06844; DUF1244
Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48299] (1)
multihelical; intertwined tetramer
1. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48300] (1)
  uperfamily
  1. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48301] (2)
Class II MHC-associated invariant chain ectoplasmic trimerization domain [48304] (1)
multihelical; intertwined trimer of identical 3-helical subunits
1. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48305] (1)
  uperfamily
  1. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48306] (1)
Aldehyde ferredoxin oxidoreductase, C-terminal domains [48309] (1)
multihelical; consists of two all-alpha domains
1. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48310] (1)
  uperfamily
  1. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48311] (2)
Acid phosphatase/Vanadium-dependent haloperoxidase [48316] (1)
multihelical; core: 5-helical bundle; binds cofactor at the beginning of third helix
1. Acid phosphatase/Vanadium-dependent haloperoxidase [48317] (3)
  uperfamily
  1. Type 2 phosphatidic acid phosphatase, PAP2 [48318] (1)
  2. Haloperoxidase (bromoperoxidase) [48321] (3)
    contains one core bundle; forms dimer
  3. Chloroperoxidase [48325] (1)
    duplication: contains two core bundles arranged as in the other family dimer
BRCA2 helical domain [81871] (1)
multihelical; contains a 3-helical bundle surrounded by several shorter helices
1. BRCA2 helical domain [81872] (1)
  uperfamily
  1. BRCA2 helical domain [81873] (2)
BRCA2 tower domain [81877] (1)
multihelical; contains a 3-helical Hin recombinase-like subdomain and two long dimerisation helices
1. BRCA2 tower domain [81878] (1)
  uperfamily
  1. BRCA2 tower domain [81879] (2)
H-NS histone-like proteins [81274] (1)
multihelical oligomeric protein; structure of whole subunit is not known yet but are probably composed of three different domains
1. H-NS histone-like proteins [81273] (1)
  available NMR structures suggest two very different dimerisation modes of the N-terminal domain
  uperfamily
  1. H-NS histone-like proteins [81272] (2)
Sigma2 domain of RNA polymerase sigma factors [88945] (1)
multihelical; consists of a conserved 4-helical core and a variable insert subdomain
1. Sigma2 domain of RNA polymerase sigma factors [88946] (1)
  uperfamily
  1. Sigma2 domain of RNA polymerase sigma factors [88947] (6)
DNA repair protein MutS, domain III [48333] (1)
multihelical; consists of 2 all-alpha subdomains
1. DNA repair protein MutS, domain III [48334] (1)
  uperfamily
  1. DNA repair protein MutS, domain III [48335] (2)
Helical scaffold and wing domains of SecA [81885] (1)
multihelical; consists of 2 all-alpha subdomains
1. Helical scaffold and wing domains of SecA [81886] (1)
  uperfamily
  1. Helical scaffold and wing domains of SecA [81887] (2)
all-alpha NTP pyrophosphatases [101385] (1)
multihelical: dimeric 4-helical bundle surrounded by other helices; oligomerizes further in a tetramer
1. all-alpha NTP pyrophosphatases [101386] (4)
  basic module consist of 5 active site-forming helices; four from one subunit/structural repeat; the fifth from the other subunit/repeat
  uperfamily
  1. MazG-like [116993] (3)
    Pfam 03819
  2. AF0060-like [140794] (1)
    consists of a single member with an orphan sequence; "circular permutation" of putative active site residues: the catalytic lysine resides in the N-terminal helix instead of the missing in this family C-terminal helix; probable biological unit is a tertramer, distinct from the MazG family tetramer
  3. Type II deoxyuridine triphosphatase [101387] (2)
    one subunit comprises two degenerate structural repeats, organised into the "rigid" and "mobile" subdomains
  4. HisE-like (PRA-PH) [140797] (5)
    Pfam 01503
Hsp90 co-chaperone CDC37 [101390] (1)
multihelical; consists of 2 all-alpha subdomains connected by a long helix
1. Hsp90 co-chaperone CDC37 [101391] (1)
  uperfamily
  1. Hsp90 co-chaperone CDC37 [101392] (1)
Nop domain [89123] (1)
multihelical; array of longer and shorter helices; contains an alpha-hairpin dimerisation subdomain
1. Nop domain [89124] (1)
  uperfamily
  1. Nop domain [89125] (2)
    putative snoRNA binding domain
YidB-like [140803] (1)
multihelical; three strings of short helices are packed across one longer helix
1. YidB-like [140804] (1)
  uperfamily
  1. YidB-like [140805] (1)
    Pfam 06078; DUF937
Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48339] (1)
multihelical; bundle of longer and shorter helices
1. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48340] (1)
  uperfamily
  1. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48341] (1)
A virus capsid protein alpha-helical domain [48344] (1)
multihelical; three-helical bundle in the core is surrounded by non-conserved helices
1. A virus capsid protein alpha-helical domain [48345] (3)
  this domain is interrupted by a jelly-roll beta-sandwich domain
  uperfamily
  1. Orbivirus capsid [48346] (1)
  2. Phytoreovirus capsid [101395] (1)
  3. vp6, the major capsid protein of group A rotavirus [63596] (1)
P40 nucleoprotein [101398] (1)
multihelical; consists of two subdomains
1. P40 nucleoprotein [101399] (1)
  uperfamily
  1. P40 nucleoprotein [101400] (1)
Rhabdovirus nucleoprotein-like [140808] (1)
multihelical, consist of two helical domains; each domain contains a buried helix
1. Rhabdovirus nucleoprotein-like [140809] (1)
  uperfamily
  1. Rhabdovirus nucleocapsid protein [140810] (2)
    Pfam 00945; RNA-binding homooligomeric protein
GTPase activation domain, GAP [48349] (1)
multihelical
1. GTPase activation domain, GAP [48350] (2)
  uperfamily
  1. BCR-homology GTPase activation domain (BH-domain) [48351] (5)
    Pfam 00620
  2. p120GAP domain-like [48360] (2)
Ras GEF [48365] (1)
multihelical
1. Ras GEF [48366] (1)
  uperfamily
  1. Ras GEF [48367] (1)
Telomeric repeat binding factor (TRF) dimerisation domain [63599] (1)
multihelical; can be divided into an alpha-alpha superhelix domain and a long alpha-hairpin dimerization domain
1. Telomeric repeat binding factor (TRF) dimerisation domain [63600] (1)
  uperfamily
  1. Telomeric repeat binding factor (TRF) dimerisation domain [63601] (2)
Poly A polymerase C-terminal region-like [81890] (1)
multihelical; can be divided into three subdomains (neck, body and tail)
1. Poly A polymerase C-terminal region-like [81891] (1)
  the neck subdomain is an alpha-alpha superhelix; the tail subdomain is similar to the RuvA C-terminal domain-like
  uperfamily
  1. Poly A polymerase C-terminal region-like [81892] (3)
    the 'neck' domain corresponds to the C-terminal part of Pfam 01743
alpha-alpha superhelix [48370] (24)
multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
1. ARM repeat [48371] (23)
  uperfamily
  1. Armadillo repeat [48372] (9)
  2. Clathrin adaptor core protein [74771] (2)
  3. HEAT repeat [48385] (2)
    Pfam 02985
  4. MIF4G domain-like [100908] (5)
    duplication: family members contains 2 or more structurally similar domains of this fold connected by unstructured linkers
  5. PHAT domain [89129] (1)
    pseudo-HEAT repeat
  6. Mo25 protein [101407] (1)
  7. Leukotriene A4 hydrolase C-terminal domain [63608] (1)
  8. Clathrin heavy chain proximal leg segment [48390] (1)
  9. Clathrin heavy-chain linker domain [48393] (1)
  10. Leucine-rich repeat variant [48396] (1)
  11. Phoshoinositide 3-kinase (PI3K) helical domain [48399] (2)
  12. Pumilio repeat [63611] (1)
  13. Regulatory subunit H of the V-type ATPase [63614] (1)
  14. PBS lyase HEAT-like repeat [101410] (2)
    Pfam 03130
  15. BC3264-like [109965] (2)
    Pfam 06352; DUF1061
  16. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain [109968] (1)
    N-terminal part of Pfam 06272
  17. Exportin HEAT-like repeat [117002] (1)
  18. B56-like [140819] (1)
    Pfam 01603; Protein phosphatase 2A regulatory B subunit family
  19. HspBP1 domain [140822] (1)
  20. GUN4-associated domain [140825] (2)
    PfamB 089177
  21. Diap1 N-terninal region-like [140830] (1)
    contains two consequitive Pfam domains in one superhelical segment: Pfam 06371 and Pfam 06367
  22. Plakophilin 1 helical region [140833] (1)
  23. RPA1889-like [158764] (1)
    Pfam 09450; DUF2019; similar to the BC3264-like family
2. IP3 receptor type 1 binding core, domain 2 [100909] (1)
  uperfamily
  1. IP3 receptor type 1 binding core, domain 2 [81895] (1)
3. Chemosensory protein Csp2 [100910] (1)
  uperfamily
  1. Chemosensory protein Csp2 [81898] (1)
4. Sec7 domain [48425] (1)
  uperfamily
  1. Sec7 domain [48426] (6)
    Pfam 01369
5. Lipovitellin-phosvitin complex, superhelical domain [48431] (1)
  uperfamily
  1. Lipovitellin-phosvitin complex, superhelical domain [48432] (1)
6. Bacterial muramidases [48435] (1)
  uperfamily
  1. Bacterial muramidases [48436] (1)
7. Aconitase B, N-terminal domain [74778] (1)
  uperfamily
  1. Aconitase B, N-terminal domain [74779] (1)
8. HCP-like [81901] (1)
  uperfamily
  1. HCP-like [81902] (2)
    Helicobacter Cysteine-rich Protein
9. Protein prenylyltransferase [48439] (1)
  uperfamily
  1. Protein prenylyltransferase [48440] (3)
10. 14-3-3 protein [48445] (1)
  uperfamily
  1. 14-3-3 protein [48446] (5)
11. TPR-like [48452] (8)
  uperfamily
  1. Tetratricopeptide repeat (TPR) [48453] (20)
  2. Transcription factor MalT domain III [69094] (1)
  3. BTAD-like [140845] (1)
    Pfam 03704; Bacterial transcriptional activator domain
  4. PrgX C-terminal domain-like [140848] (1)
  5. Atu0120-like [158772] (1)
    Pfam 06041; DUF924
  6. SusD-like [158775] (3)
    TPR-like structure resides in the N-terminal part; the C-terminal part is structurally unique and is covered by Pfam 07980
  7. HAT/Suf repeat [158782] (1)
    includes Pfam 05843
  8. CT2138-like [158785] (1)
    probable biological unit is a homohexamer
12. ENTH/VHS domain [48464] (4)
  uperfamily
  1. ENTH domain [48465] (2)
  2. VHS domain [48468] (5)
  3. Phosphoinositide-binding clathrin adaptor, N-terminal domain [100911] (2)
  4. RPR domain (SMART 00582 ) [109975] (1)
    found in proteins involved in regulation of nuclear pre-mRNA; some sequence similarity to VHS domain
13. Translin [74784] (1)
  uperfamily
  1. Translin [74785] (2)
14. Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain [69099] (1)
  uperfamily
  1. Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain [69100] (2)
15. Arp2/3 complex 16 kDa subunit ARPC5 [69103] (1)
  uperfamily
  1. Arp2/3 complex 16 kDa subunit ARPC5 [69104] (1)
16. FliG [48029] (1)
  fragmented superhelix; consist of 3/4-helical motifs and connecting helices
  uperfamily
  1. FliG [48030] (1)
17. Cullin repeat-like [74788] (2)
  uperfamily
  1. Cullin repeat [74789] (2)
  2. Exocyst complex component [140851] (2)
    includes Pfam 03081
18. C-terminal domain of Ku80 [101420] (1)
  uperfamily
  1. C-terminal domain of Ku80 [101421] (1)
19. Hypothetical protein ST1625 [101424] (1)
  uperfamily
  1. Hypothetical protein ST1625 [101425] (1)
20. Cytochrome c oxidase subunit E [48479] (1)
  uperfamily
  1. Cytochrome c oxidase subunit E [48480] (1)
21. USP8 N-terminal domain-like [140856] (1)
  uperfamily
  1. USP8 N-terminal domain-like [140857] (1)
    PfamB 029795
22. Pseudo ankyrin repeat-like [140860] (1)
  contains three helices per turn of the superhelix
  uperfamily
  1. Pseudo ankyrin repeat [140861] (1)
    one repeat consist of 3 helices; there are similarities in the repeat sequence and assembly with the ankyrin repeat (scop_fa 48404)
23. TROVE domain-like [140864] (1)
  consist of two superhelical sections arranged like a horse-shoe
  uperfamily
  1. TROVE domain-like [140865] (1)
    Pfam 05731
24. MgtE N-terminal domain-like [158791] (1)
  made of short helices; approximately 2.5 helices per turn of superhelix
  1. MgtE N-terminal domain-like [158792] (2)
    Pfam 03448
GUN4-like [140868] (1)
multihelical; open array, trapping inside an extended region before the C-terminal helix
1. GUN4-like [140869] (1)
  uperfamily
  1. GUN4-like [140870] (2)
    Pfam 05419
Lipoxigenase [48483] (1)
multihelical
large nearly all-alpha domain
1. Lipoxigenase [48484] (2)
  uperfamily
  1. Plant lipoxigenases [48485] (2)
  2. Animal lipoxigenases [48489] (1)
gene 59 helicase assembly protein [48492] (1)
multihelical; consists of two all-alpha subdomains
1. gene 59 helicase assembly protein [48493] (1)
  uperfamily
  1. gene 59 helicase assembly protein [48494] (1)
Tetracyclin repressor-like, C-terminal domain [48497] (1)
multihelical; interlocked (homo)dimer
1. Tetracyclin repressor-like, C-terminal domain [48498] (1)
  uperfamily
  1. Tetracyclin repressor-like, C-terminal domain [48499] (34)
Skp1 dimerisation domain-like [81384] (1)
multihelical; interlocked heterodimer with F-box proteins
1. Skp1 dimerisation domain-like [81382] (1)
  uperfamily
  1. Skp1 dimerisation domain-like [81380] (2)
F-box domain [81385] (1)
multihelical; interlocked heterodimer with the Skp1 dimerisation domain
1. F-box domain [81383] (1)
  uperfamily
  1. F-box domain [81381] (4)
Nuclear receptor ligand-binding domain [48507] (1)
multihelical; 3 layers or orthogonally packed helices
1. Nuclear receptor ligand-binding domain [48508] (1)
  uperfamily
  1. Nuclear receptor ligand-binding domain [48509] (44)
Phospholipase C/P1 nuclease [48536] (1)
multihelical
1. Phospholipase C/P1 nuclease [48537] (2)
  duplication: all chain but the N-terminal helix forms two structural repeats
  uperfamily
  1. Phospholipase C [48538] (3)
  2. P1 nuclease [48543] (1)
ATP-dependent DNA ligase DNA-binding domain [117017] (1)
multihelical; duplication: contains two intertwined structural repeats related by pseudo twofold symmetry
1. ATP-dependent DNA ligase DNA-binding domain [117018] (1)
  uperfamily
  1. ATP-dependent DNA ligase DNA-binding domain [117019] (1)
    Pfam 04675
DNA primase DnaG, C-terminal domain [117022] (1)
multihelical; segment-swapped dimer
1. DNA primase DnaG, C-terminal domain [117023] (1)
  uperfamily
  1. DNA primase DnaG, C-terminal domain [117024] (1)
PriB N-terminal domain-like [140913] (1)
multihelical bundle; contains buried central helix; also includes the PriA interface-forming insert subdomain (alpha+beta)
1. PriB N-terminal domain-like [140914] (1)
  uperfamily
  1. PriB N-terminal domain-like [140915] (1)
VPS9 domain [109992] (1)
multihelical; consist of two subdomains
1. VPS9 domain [109993] (1)
  uperfamily
  1. VPS9 domain [109994] (1)
    Pfam 02204
Triger factor/SurA peptide-binding domain-like [109997] (1)
multihelical; irregular array of long and short helices
1. Triger factor/SurA peptide-binding domain-like [109998] (2)
  there are sequence and functional similarities between the families, but their structural similarity is obscured by conformational flexibility (in the TF family)
  uperfamily
  1. TF C-terminus [109999] (2)
    Pfam 05698; includes the upstream linker region not covered by the Pfam model
  2. Porin chaperone SurA, peptide-binding domain [81828] (1)
DNA terminal protein [140918] (1)
multihelical, open array; contains the C-terminal four-helical bundle, left-handed superhelix
1. DNA terminal protein [140919] (1)
  uperfamily
  1. DNA terminal protein [140920] (1)
    Pfam 05435
Glycolipid transfer protein, GLTP [110003] (1)
multihelical; 2 layers or orthogonally packed helices
1. Glycolipid transfer protein, GLTP [110004] (1)
  uperfamily
  1. Glycolipid transfer protein, GLTP [110005] (1)
Hypothetical protein MG354 [110008] (1)
multihelical bundle; contains buried central helix
1. Hypothetical protein MG354 [110009] (1)
  uperfamily
  1. Hypothetical protein MG354 [110010] (1)
Duffy binding domain-like [140923] (1)
consist of two subdomains, each containing a three-helical bundle
1. Duffy binding domain-like [140924] (1)
  uperfamily
  1. Duffy binding domain [140925] (2)
    Pfam 05424
Fic-like [140930] (1)
multihelical; one central helix is surrounded by seven helices
1. Fic-like [140931] (1)
  uperfamily
  1. Fic-like [140932] (2)
    Pfam 02661; the conserved motif HPFXXGNG is at the N-terminus of the central helix
Her-1 [110013] (1)
multihelical; consists of two topologically similar alpha-helical bundles
1. Her-1 [110014] (1)
  uperfamily
  1. Her-1 [110015] (1)
ERO1-like [110018] (1)
multihelical; consists of 2 four-helical bundles
1. ERO1-like [110019] (1)
  similar active site architecture to scop_sf 69000
  uperfamily
  1. ERO1-like [110020] (1)
    Pfam 04137
Serum albumin-like [48551] (1)
multihelical; one domain consists of two similar disulfide-linked subdomains
1. Serum albumin-like [48552] (1)
  uperfamily
  1. Serum albumin-like [48553] (2)
L-aspartase-like [48556] (1)
multihelical, consists of three all-alpha domains
1. L-aspartase-like [48557] (2)
  uperfamily
  1. L-aspartase/fumarase [48558] (14)
  2. HAL/PAL-like [48572] (3)
    Pfam 00221
Formin homology 2 domain (FH2 domain) [101446] (1)
multihelical, consists of three all-alpha domains
1. Formin homology 2 domain (FH2 domain) [101447] (1)
  uperfamily
  1. Formin homology 2 domain (FH2 domain) [101448] (2)
Terpenoid synthases [48575] (1)
multihelical; core: 8 helices (C-J) are arranged in 2 parallel layers
1. Terpenoid synthases [48576] (5)
  duplication: two metal-binding sites are related by a pseudo dyad that also relates helices C-F to helices G-J
  uperfamily
  1. Isoprenyl diphosphate synthases [48577] (5)
  2. Squalene synthase [48580] (1)
  3. Terpenoid cyclase C-terminal domain [48583] (2)
  4. Aristolochene/pentalenene synthase [48586] (2)
  5. Trichodiene synthase [69113] (1)
GroEL equatorial domain-like [48591] (1)
multihelical; 8 helices arranged in 2 parallel layers
1. GroEL equatorial domain-like [48592] (2)
  duplication: two 4-helical subdomains are related by a pseudo dyad passing through the ATP-binding site
  uperfamily
  1. GroEL chaperone, ATPase domain [48593] (4)
  2. Group II chaperonin (CCT, TRIC), ATPase domain [48596] (3)
TorD-like [89154] (1)
multihelical; bundle
1. TorD-like [89155] (1)
  uperfamily
  1. TorD-like [89156] (4)
    Pfam 06192
Chorismate mutase II [48599] (1)
multihelical; core: 6 helices, bundle
1. Chorismate mutase II [48600] (4)
  uperfamily
  1. Dimeric chorismate mutase [48601] (4)
    intertwined homodimer of 3-helical subunits
  2. Allosteric chorismate mutase [48604] (1)
    duplication: 2 weak structural repeats resembling subunits of E. coli protein
  3. monomeric chorismate mutase [140942] (1)
    "un-swapped" four-helical relative of the homodimeric chorismate mutase domain
  4. Secreted chorismate mutase-like [140945] (1)
    duplication; two structural repeats, like in the yeast enzyme, but with a different location of the remaining active site
Peridinin-chlorophyll protein [48607] (1)
multihelical: forms a boat-shaped protein shell around cofactors
1. Peridinin-chlorophyll protein [48608] (1)
  duplication: consists of two 8-helical repeats
  uperfamily
  1. Peridinin-chlorophyll protein [48609] (1)
Heme oxygenase-like [48612] (1)
multihelical; bundle
1. Heme oxygenase-like [48613] (4)
  duplication: contains two structural repeats of 3-helical motif
  uperfamily
  1. Eukaryotic type heme oxygenase [48614] (5)
  2. Heme oxygenase HemO (PigA) [63627] (2)
  3. TENA/THI-4 [101458] (8)
    Pfam 03070; HO-related family lacking the heme-binding site
  4. PqqC-like [101463] (2)
    Pfam 05312
Indolic compounds 2,3-dioxygenase-like [140958] (1)
multihelical; bundle, contains interrupted helices
1. Indolic compounds 2,3-dioxygenase-like [140959] (2)
  contains heme-dependent enzymes
  uperfamily
  1. Bacterial tryptophan 2,3-dioxygenase [140960] (1)
    Pfam 03301
  2. Indoleamine 2,3-dioxygenase-like [140963] (2)
    Pfam 01231; contains extra N-terminal all-alpha subdomain of similar fold to the GST C-terminal domain (scop_cf 47615)
AhpD-like [69117] (1)
multihelical; contains 4-helical bundle and 2-helical arm
1. AhpD-like [69118] (4)
  probable biological unit contains six domains of this fold arranged with 32 symmetry
  uperfamily
  1. CMD-like [101468] (2)
    Pfam 02627; hexamer of single-domain subunits
  2. AhpD [69119] (2)
    duplication: two-domain subunits form a helix-swapped trimer
  3. Atu0492-like [140970] (5)
    duplication: similar subunit structure to the AhpD family, but the putative active site is conserved in different relative location; new hexameric architecture; similar dimeric interface to the CMD-like family
  4. TTHA0727-like [140975] (2)
    similar to the CMD-like family by the subunit sequence and hexameric architecture; the segment-swapped subunit fold is similar to the AhpD domains
Double Clp-N motif [81922] (1)
multihelical; array
1. Double Clp-N motif [81923] (1)
  duplication: contains two structural repeats of 4-helical motif
  uperfamily
  1. Double Clp-N motif [81924] (3)
Orange carotenoid protein, N-terminal domain [81929] (1)
multihelical; array
1. Orange carotenoid protein, N-terminal domain [81930] (1)
  duplication: contains four structural repeats arranged into two intertwined 4-helical subdomains
  uperfamily
  1. Orange carotenoid protein, N-terminal domain [81931] (1)
DhaL-like [101472] (1)
multihelical; bundle
1. DhaL-like [101473] (1)
  uperfamily
  1. DhaL-like [101474] (2)
ADP-ribosylglycohydrolase [101477] (1)
multihelical; bundle
1. ADP-ribosylglycohydrolase [101478] (1)
  uperfamily
  1. ADP-ribosylglycohydrolase [101479] (1)
    Pfam 03747
Topoisomerase V catalytic domain-like [140978] (1)
multihelical; irregular array; contains small amount of beta-structure and a 3-helical bundle with a variant homeofomain-like fold and HTH motif (scop_cf 46688)
1. Topoisomerase V catalytic domain-like [140979] (1)
  uperfamily
  1. Topoisomerase V catalytic domain-like [140980] (1)
PTPA-like [140983] (1)
multihelical
1. PTPA-like [140984] (1)
  uperfamily
  1. PTPA-like [140985] (2)
    Pfam 03095
Tex N-terminal region-like [158831] (1)
multihelical; irregular array of long and short helices; can be divided into several subdomains
1. Tex N-terminal region-like [158832] (1)
  1. Tex N-terminal region-like [158833] (1)
    Pfam 09371
AGR_C_984p-like [158836] (1)
multihelical, consists of two subdomains; duplication: there are two 5-helical structural repeats, one in each subdomain
1. AGR_C_984p-like [158837] (1)
  1. AGR_C_984p-like [158838] (1)
    Pfam 06748; DUF1217
PMT central region-like [158841] (1)
multihelical; comprises two four-helical bundles of different topologies and an irregular helical array packed against a small beta-sheet
1. PMT central region-like [158842] (1)
  1. PMT central region-like [158843] (1)
FtsH protease domain-like [140989] (1)
array of 6 helices and a 2-stranded beta-ribbon
1. FtsH protease domain-like [140990] (1)
  contains zincin-like (scop_sf 55486) metal-binding motif HExxH, embedded into a topologically different fold
  uperfamily
  1. FtsH protease domain-like [140991] (2)
    Pfam 01434; Peptidase family M41
Gametocyte protein Pfg27 [89161] (1)
multihelical; bundle
1. Gametocyte protein Pfg27 [89162] (1)
  duplication: contains two structural repeats of four helices each
  uperfamily
  1. Gametocyte protein Pfg27 [89163] (1)
N-terminal domain of bifunctional PutA protein [81934] (1)
multihelical; array
1. N-terminal domain of bifunctional PutA protein [81935] (1)
  uperfamily
  1. N-terminal domain of bifunctional PutA protein [81936] (1)
Cysteine alpha-hairpin motif [47071] (1)
core: alpha-hairpin crosslinked with two disulfides
1. Cysteine alpha-hairpin motif [47072] (2)
  uperfamily
  1. p8-MTCP1 [47073] (1)
  2. COX17-like [117033] (1)
    Pfam 05051
Phospholipase A2, PLA2 [48618] (1)
common core: 2 helices, disulfide-linked, and a calcium-binding loop
1. Phospholipase A2, PLA2 [48619] (3)
  uperfamily
  1. Vertebrate phospholipase A2 [48623] (39)
  2. Insect phospholipase A2 [48620] (1)
  3. Prokaryotic phospholipase A2 [63630] (1)
Fungal elicitin [48646] (1)
5 helices: irregular disulfide-linked array; also contains a small beta-hairpin
1. Fungal elicitin [48647] (1)
  uperfamily
  1. Fungal elicitin [48648] (2)
Tetraspanin [48651] (1)
5 helices: irregular disulfide-linked array; form homodimer
1. Tetraspanin [48652] (1)
  uperfamily
  1. Tetraspanin [48653] (1)
GDNF receptor-like [110034] (1)
5 helices: irregular disulfide-linked array; topological similarity to the Fungal elicitin fold (scop_cf 48646)
1. GDNF receptor-like [110035] (1)
  uperfamily
  1. GDNF receptor-like [110036] (1)
    Pfam 02351
FinO-like [48656] (1)
6 helices: irregular non-globular array; also contains two small beta-hairpins
1. FinO-like [48657] (1)
  uperfamily
  1. FinO-like [48658] (2)
Nuclear receptor coactivator interlocking domain [69124] (1)
3 helices, non-globular array; forms interlocked heterodimers with its targets
1. Nuclear receptor coactivator interlocking domain [69125] (1)
  not a true superfamily
  uperfamily
  1. Nuclear receptor coactivator interlocking domain [69126] (3)
Hermes dimerisation domain [140995] (1)
multihelical, intertwinned dimer of two 4-helical strings
1. Hermes dimerisation domain [140996] (1)
  uperfamily
  1. Hermes dimerisation domain [140997] (1)
Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101488] (1)
5 helices, non-globular array; wraps around the N-terminal tail of its target
1. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101489] (1)
  not a true superfamily
  uperfamily
  1. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101490] (1)
Non-globular all-alpha subunits of globular proteins [48661] (14)
not a true fold
1. Ribosomal protein L39e [48662] (1)
  interrupted alpha-helix
  uperfamily
  1. Ribosomal protein L39e [48663] (1)
2. Methanol dehydrogenase subunit [48666] (1)
  consists of single alpha-helix and irregular N-terminal tail
  uperfamily
  1. Methanol dehydrogenase subunit [48667] (3)
3. Transducin (heterotrimeric G protein), gamma chain [48670] (1)
  long alpha-helix interrupted in the middle
  uperfamily
  1. Transducin (heterotrimeric G protein), gamma chain [48671] (2)
4. Fe-only hydrogenase smaller subunit [48674] (1)
  uperfamily
  1. Fe-only hydrogenase smaller subunit [48675] (1)
5. Moesin tail domain [48678] (1)
  uperfamily
  1. Moesin tail domain [48679] (1)
6. Proteinase A inhibitor IA3 [48686] (1)
  uperfamily
  1. Proteinase A inhibitor IA3 [48687] (1)
7. Epsilon subunit of mitochondrial F1F0-ATP synthase [48690] (1)
  uperfamily
  1. Epsilon subunit of mitochondrial F1F0-ATP synthase [48691] (1)
8. Quinohemoprotein amine dehydrogenase C chain [69131] (1)
  uperfamily
  1. Quinohemoprotein amine dehydrogenase C chain [69132] (2)
9. Stathmin [101494] (1)
  single long helix crosslinking four tubulin subunits
  uperfamily
  1. Stathmin [101495] (1)
10. Anti-sigma factor FlgM [101498] (1)
  uperfamily
  1. Anti-sigma factor FlgM [101499] (1)
11. Glu-tRNAGln amidotransferase C subunit [141000] (1)
  uperfamily
  1. Glu-tRNAGln amidotransferase C subunit [141001] (1)
    Pfam 02686
12. RelB-like [141004] (1)
  wraps around RelE subunit
  uperfamily
  1. RelB-like [141005] (1)
13. Lag-3 N-terminal region [158851] (1)
  long kinked helix, part of the CSL-Notch-Mastermind ternary complex
  1. Lag-3 N-terminal region [158852] (1)
14. Lipase chaperone-like [158855] (1)
  open single layer scaffold of 11 helices, which engulfs the substrate protein
  1. Lipase chaperone LifO-like [158856] (1)
    Pfam 03280
Multiheme cytochromes [48694] (1)
variable number of helices and little beta structure; not a true fold
1. Multiheme cytochromes [48695] (3)
  duplication: contains multiple CxxCH motifs
  uperfamily
  1. Cytochrome c3-like [48696] (13)
  2. Photosynthetic reaction centre (cytochrome subunit) [48707] (2)
    consists of four heme-binding repeats
  3. Di-heme elbow motif [48711] (13)
    the main characteristic feature of this motif is the packing of its two hemes
    many members contains one or more complete motifs flanked by incomplete motifs and/or other domains