Fold: Sm-like fold

core: barrel, open; n*=4, S*=8; meander; SH3-like topology

Lineage:

1. Root: scop
2. Class: All beta proteins [48724]
3. Fold: Sm-like fold [50181]
   core: barrel, open; n*=4, S*=8; meander; SH3-like topology

Superfamilies:

1. Sm-like ribonucleoproteins [50182] (6)
   uperfamily
   1. Sm motif of small nuclear ribonucleoproteins, SNRNP [50183] (13)
      forms homo and heteroheptameric ring structures
      1. D1 core SNRNP protein [50184]
         1. Human (Homo sapiens) [TaxId: 9606] [50185] (1)
            1. 1b34
               1. chain a [24796]
      2. D2 core SNRNP protein [50186]
         1. Human (Homo sapiens) [TaxId: 9606] [50187] (1)
            1. 1b34
               1. chain b [24797]
      3. D3 core SNRNP protein [50188]
         1. Human (Homo sapiens) [TaxId: 9606] [50189] (1)
            1. 1d3b
               CASP3
               1. chain a [24798]
               2. chain c [24799]
               3. chain e [24800]
               4. chain g [24801]
               5. chain i [24802]
               6. chain k [24803]
      4. B core SNRNP protein [50190]
         1. Human (Homo sapiens) [TaxId: 9606] [50191] (1)
            1. 1d3b
               CASP3
               1. chain b [24804]
               2. chain d [24805]
               3. chain f [24806]
               4. chain h [24807]
               5. chain j [24808]
               6. chain l [24809]
      5. Small nuclear ribonucleoprotein F, Smf [82087]
         1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82088] (2)
            1. 1n9r
               1. chain a [80344]
               2. chain b [80345]
               3. chain c [80346]
               4. chain d [80347]
               5. chain e [80348]
               6. chain f [80349]
               7. chain g [80350]
            2. 1n9s
               1. chain a [80351]
               2. chain b [80352]
               3. chain c [80353]
               4. chain d [80354]
               5. chain e [80355]
               6. chain f [80356]
               7. chain g [80357]
               8. chain h [80358]
               9. chain i [80359]
               10. chain j [80360]
               11. chain k [80361]
               12. chain l [80362]
               13. chain m [80363]
               14. chain n [80364]
      6. Archaeal homoheptameric Sm protein [63758]
         1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63759] (5)
            MTH649, smap1
            1. 1mgq
               1. chain a [79099]
               2. chain b [79100]
               3. chain c [79101]
               4. chain d [79102]
               5. chain e [79103]
               6. chain f [79104]
               7. chain g [79105]
            2. 1jbm
               structural genomics
               complexed with acy, edo
               1. chain a [84143]
               2. chain b [84144]
               3. chain c [84145]
               4. chain d [84146]
               5. chain e [84147]
               6. chain f [84148]
               7. chain g [84149]
            3. 1i81
               1. chain a [61930]
               2. chain b [61931]
               3. chain c [61932]
               4. chain d [61933]
               5. chain e [61934]
               6. chain f [61935]
               7. chain g [61936]
            4. 1loj
               complexed with mpd, u, uri
               1. chain a [84650]
               2. chain b [84651]
               3. chain c [84652]
               4. chain d [84653]
               5. chain e [84654]
               6. chain f [84655]
               7. chain g [84656]
               8. chain h [84657]
               9. chain i [84658]
               10. chain j [84659]
               11. chain k [84660]
               12. chain l [84661]
               13. chain m [84662]
               14. chain n [84663]
            5. 1jri
               complexed with cl, edo
               1. chain a [67121]
               2. chain b [67122]
               3. chain c [67123]
               4. chain d [67124]
               5. chain e [67125]
               6. chain f [67126]
               7. chain g [67127]
               8. chain h [67128]
               9. chain i [67129]
               10. chain j [67130]
               11. chain k [67131]
               12. chain l [67132]
               13. chain m [67133]
               14. chain n [67134]
         2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [63760] (2)
            smap1
            1. 1i8f
               complexed with gol
               1. chain a [61959]
               2. chain b [61960]
               3. chain c [61961]
               4. chain d [61962]
               5. chain e [61963]
               6. chain f [61964]
               7. chain g [61965]
            2. 1lnx
               complexed with acy, gol, uri
               1. chain a [84642]
               2. chain b [84643]
               3. chain c [84644]
               4. chain d [84645]
               5. chain e [84646]
               6. chain f [84647]
               7. chain g [84648]
         3. Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234] [63761] (2)
            1. 1i4k
               complexed with cit
               1. chain a [61692]
               2. chain b [61693]
               3. chain c [61694]
               4. chain d [61695]
               5. chain e [61696]
               6. chain f [61697]
               7. chain g [61698]
               8. chain h [61699]
               9. chain i [61700]
               10. chain j [61701]
               11. chain k [61702]
               12. chain l [61703]
               13. chain m [61704]
               14. chain n [61705]
               15. chain o [61706]
               16. chain p [61707]
               17. chain q [61708]
               18. chain r [61709]
               19. chain s [61710]
               20. chain t [61711]
               21. chain u [61712]
               22. chain v [61713]
               23. chain w [61714]
               24. chain x [61715]
               25. chain y [61716]
               26. chain z [61717]
               27. chain 1 [61690]
               28. chain 2 [61691]
            2. 1i5l
               complexed with short poly-U RNA
               complexed with uri
               1. chain a [61791]
               2. chain b [61792]
               3. chain c [61793]
               4. chain d [61794]
               5. chain e [61795]
               6. chain f [61796]
               7. chain g [61797]
               8. chain h [61798]
               9. chain i [61799]
               10. chain j [61800]
               11. chain k [61801]
               12. chain l [61802]
               13. chain m [61803]
               14. chain n [61804]
         4. Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234] [74938] (1)
            1. 1ljo
               complexed with acy, cd; mutant
               1. chain a [73941]
         5. Archaeon Pyrococcus abyssi [TaxId: 29292] [82089] (2)
            1. 1h64
               1. chain a [76677]
               2. chain b [76678]
               3. chain c [76679]
               4. chain d [76680]
               5. chain e [76681]
               6. chain f [76682]
               7. chain g [76683]
               8. chain h [76684]
               9. chain i [76685]
               10. chain j [76686]
               11. chain k [76687]
               12. chain l [76688]
               13. chain m [76689]
               14. chain n [76690]
               15. chain o [76691]
               16. chain p [76692]
               17. chain q [76693]
               18. chain r [76694]
               19. chain s [76695]
               20. chain t [76696]
               21. chain u [76697]
               22. chain v [76698]
               23. chain w [76699]
               24. chain x [76700]
               25. chain y [76701]
               26. chain z [76702]
               27. chain 1 [76675]
               28. chain 2 [76676]
            2. 1m8v
               complexed with a uridine heptamer
               complexed with ca, u
               1. chain a [78814]
               2. chain b [78815]
               3. chain c [78816]
               4. chain d [78817]
               5. chain e [78818]
               6. chain f [78819]
               7. chain g [78820]
               8. chain h [78821]
               9. chain i [78822]
               10. chain j [78823]
               11. chain k [78824]
               12. chain l [78825]
               13. chain m [78826]
               14. chain n [78827]
         6. Sulfolobus solfataricus [TaxId: 2287] [141290] (14)
            SQ Q97ZQ0 1-76
            SnRNP-2
            1. 1th7
               1. region a:3-78 [119264]
            2. 1th7
               automatically matched to 1TH7 A:3-78
               1. region b:3-78 [119265]
            3. 1th7
               automatically matched to 1TH7 A:3-78
               1. region c:3-78 [119266]
            4. 1th7
               automatically matched to 1TH7 A:3-78
               1. region d:3-78 [119267]
            5. 1th7
               automatically matched to 1TH7 A:3-78
               1. region e:3-78 [119268]
            6. 1th7
               automatically matched to 1TH7 A:3-78
               1. region f:3-78 [119269]
            7. 1th7
               automatically matched to 1TH7 A:3-78
               1. region g:3-78 [119270]
            8. 1th7
               automatically matched to 1TH7 A:3-78
               1. region h:3-78 [119271]
            9. 1th7
               automatically matched to 1TH7 A:3-78
               1. region i:3-78 [119272]
            10. 1th7
                automatically matched to 1TH7 A:3-78
                1. region j:3-78 [119273]
            11. 1th7
                automatically matched to 1TH7 A:3-78
                1. region k:3-78 [119274]
            12. 1th7
                automatically matched to 1TH7 A:3-78
                1. region l:3-78 [119275]
            13. 1th7
                automatically matched to 1TH7 A:3-78
                1. region m:3-78 [119276]
            14. 1th7
                automatically matched to 1TH7 A:3-78
                1. region n:3-78 [119277]
      7. Sm-Like archaeal protein Smap3 [89317]
         contains additional C-terminal alpha+beta domain
         1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [89318] (1)
            1. 1m5q
               complexed with acy, cd, gol, mse, na
               1. chain a [84810]
               2. chain b [84811]
               3. chain c [84812]
               4. chain d [84813]
               5. chain e [84814]
               6. chain f [84815]
               7. chain g [84816]
               8. chain h [84817]
               9. chain i [84818]
               10. chain j [84819]
               11. chain k [84820]
               12. chain l [84821]
               13. chain m [84822]
               14. chain n [84823]
               15. chain o [84824]
               16. chain p [84825]
               17. chain q [84826]
               18. chain r [84827]
               19. chain s [84828]
               20. chain t [84829]
               21. chain u [84830]
               22. chain v [84831]
               23. chain w [84832]
               24. chain x [84833]
               25. chain y [84834]
               26. chain z [84835]
               27. chain 1 [84808]
               28. chain 2 [84809]
      8. U6 snRNA-associated sm-like protein LSM5 [141291]
         1. Cryptosporidium parvum [TaxId: 5807] [141292] (2)
            SQ Q5CXX3 24-115
            1. 2fwk
               1. region a:24-115 [134245]
            2. 2fwk
               automatically matched to 2FWK A:24-115
               1. region b:26-113 [134246]
   2. Pleiotropic translational regulator Hfq [74939] (3)
      forms homohexameric ring structures
      1. Pleiotropic translational regulator Hfq [74940]
         1. Staphylococcus aureus [TaxId: 1280] [74941] (2)
            1. 1kq1
               complexed with acy
               1. chain a [72848]
               2. chain b [72849]
               3. chain h [72850]
               4. chain i [72851]
               5. chain k [72852]
               6. chain m [72853]
               7. chain s [72856]
               8. chain t [72857]
               9. chain y [72859]
               10. chain n [72854]
               11. chain r [72855]
               12. chain w [72858]
            2. 1kq2
               1. chain a [72860]
               2. chain b [72861]
               3. chain h [72862]
               4. chain i [72863]
               5. chain k [72864]
               6. chain m [72865]
         2. Escherichia coli [TaxId: 562] [89319] (1)
            1. 1hk9
               1. chain a [83541]
               2. chain b [83542]
               3. chain c [83543]
               4. chain d [83544]
               5. chain e [83545]
               6. chain f [83546]
         3. Pseudomonas aeruginosa [TaxId: 287] [141293] (12)
            SQ Q9HUM0 6-71
            1. 1u1s
               1. region a:6-71 [119451]
            2. 1u1s
               automatically matched to 1U1S A:6-71
               1. region b:6-70 [119452]
            3. 1u1s
               automatically matched to 1U1S A:6-71
               1. region c:6-69 [119453]
            4. 1u1s
               automatically matched to 1U1S A:6-71
               1. region d:6-71 [119454]
            5. 1u1s
               automatically matched to 1U1S A:6-71
               1. region e:6-69 [119455]
            6. 1u1s
               automatically matched to 1U1S A:6-71
               1. region f:6-69 [119456]
            7. 1u1t
               automatically matched to 1U1S A:6-71
               1. region a:6-71 [119457]
            8. 1u1t
               automatically matched to 1U1S A:6-71
               1. region b:6-70 [119458]
            9. 1u1t
               automatically matched to 1U1S A:6-71
               1. region c:6-69 [119459]
            10. 1u1t
                automatically matched to 1U1S A:6-71
                1. region d:6-71 [119460]
            11. 1u1t
                automatically matched to 1U1S A:6-71
                1. region e:6-71 [119461]
            12. 1u1t
                automatically matched to 1U1S A:6-71
                1. region f:6-70 [119462]
   3. Mechanosensitive channel protein MscS (YggB), middle domain [82090] (1)
      1. Mechanosensitive channel protein MscS (YggB), middle domain [82091]
         forms homoheptameric ring structure very similar to those of the archaeal and eukaryotic Sm proteins
         1. Escherichia coli [TaxId: 562] [82092] (14)
            1. 2vv5
               automatically matched to d2oaua1
               mutant
               1. region a:113-179 [153613]
            2. 2vv5
               automatically matched to d2oaua1
               mutant
               1. region b:113-179 [153616]
            3. 2vv5
               automatically matched to d2oaua1
               mutant
               1. region c:113-179 [153619]
            4. 2vv5
               automatically matched to d2oaua1
               mutant
               1. region d:113-179 [153622]
            5. 2vv5
               automatically matched to d2oaua1
               mutant
               1. region e:113-179 [153625]
            6. 2vv5
               automatically matched to d2oaua1
               mutant
               1. region f:113-179 [153628]
            7. 2vv5
               automatically matched to d2oaua1
               mutant
               1. region g:113-179 [153631]
            8. 2oau
               automatically matched to d1mxma1
               1. region a:113-179 [138978]
            9. 2oau
               automatically matched to d1mxma1
               1. region b:113-179 [138981]
            10. 2oau
                automatically matched to d1mxma1
                1. region c:113-179 [138984]
            11. 2oau
                automatically matched to d1mxma1
                1. region d:113-179 [138987]
            12. 2oau
                automatically matched to d1mxma1
                1. region e:113-179 [138990]
            13. 2oau
                automatically matched to d1mxma1
                1. region f:113-179 [138993]
            14. 2oau
                automatically matched to d1mxma1
                1. region g:113-179 [138996]
   4. PF1955-like [141294] (1)
      homohexadecameric assembly: two stacked octameric rings
      1. Hypothetical protein PF1955 [141295]
         1. Pyrococcus furiosus [TaxId: 2261] [141296] (4)
            SQ Q8TZN2 5-70
            1. 1ycy
               1. region a:5-70 [122970]
            2. 1ycy
               automatically matched to 1YCY A:5-70
               1. region b:5-70 [122971]
            3. 1ycy
               automatically matched to 1YCY A:5-70
               1. region c:5-70 [122972]
            4. 1ycy
               automatically matched to 1YCY A:5-70
               1. region d:5-70 [122973]
   5. LSM14 N-terminal domain-like [141297] (1)
      1. LSM14 homolog A (Lsm14a) [141298]
         1. Zebrafish (Danio rerio) [TaxId: 7955] [141299] (2)
            SQ Q6P111 6-85
            1. 2vxf
               automatically matched to d2fb7a1
               mutant
               1. region a:6-85 [153679]
            2. 2fb7
               1. region a:16-95 [133238]
   6. YgdI/YgdR-like [159052] (6)
      Pfam 06004; DUF903, putative lipoprotein; both homohexameric and homoheptameric ring assemblies are observed in the crystals
      1. Uncharacterized protein SO0963 [159053]
         1. Shewanella oneidensis [TaxId: 70863] [159054] (2)
            SQ Q8EI81 25-76
            1. 2rb6
               1. region a:25-76 [151844]
            2. 2rb6
               automatically matched to 2RB6 A:25-76
               1. region b:25-76 [151845]
      2. Uncharacterized protein YgdI [159055]
         1. Salmonella typhimurium [TaxId: 90371] [159056] (6)
            SQ Q7CPV8 23-75
            1. 2ra2
               1. region a:4-56 [151811]
            2. 2ra2
               automatically matched to 2RA2 A:4-56
               1. region b:4-56 [151812]
            3. 2ra2
               automatically matched to 2RA2 A:4-56
               1. region c:4-56 [151813]
            4. 2ra2
               automatically matched to 2RA2 A:4-56
               1. region d:4-56 [151814]
            5. 2ra2
               automatically matched to 2RA2 A:4-56
               1. region e:4-56 [151815]
            6. 2ra2
               automatically matched to 2RA2 A:4-56
               1. region f:4-55 [151816]
      3. Uncharacterized protein ECA1013 [159057]
         1. Erwinia carotovora [TaxId: 554] [159058] (7)
            SQ Q6D8G1 21-73
            1. 3bdu
               1. region a:2-54 [155154]
            2. 3bdu
               automatically matched to 3BDU A:2-54
               1. region b:2-53 [155155]
            3. 3bdu
               automatically matched to 3BDU A:2-54
               1. region c:2-53 [155156]
            4. 3bdu
               automatically matched to 3BDU A:2-54
               1. region d:2-53 [155157]
            5. 3bdu
               automatically matched to 3BDU A:2-54
               1. region e:2-54 [155158]
            6. 3bdu
               automatically matched to 3BDU A:2-54
               1. region f:2-53 [155159]
            7. 3bdu
               automatically matched to 3BDU A:2-54
               1. region g:2-53 [155160]
      4. Putative outer membrane lipoprotein STM1585 [159059]
         1. Salmonella typhimurium [TaxId: 90371] [159060] (3)
            SQ Q7CQI7 22-73
            1. 2rd1
               1. region a:22-73 [151915]
            2. 2rd1
               automatically matched to 2RD1 A:22-73
               1. region b:22-73 [151916]
            3. 2rd1
               automatically matched to 2RD1 A:22-73
               1. region c:22-73 [151917]
      5. Uncharacterized protein PSPPH2109 [159061]
         1. Pseudomonas syringae [TaxId: 317] [159062] (1)
            SQ Q48JU9 23-74
            1. 2k57
               1. region a:2-53 [148272]
      6. Hypothetical lipoprotein YgdR [159063]
         1. Escherichia coli [TaxId: 562] [159064] (1)
            SQ P65294 23-72
            1. 2jn0
               1. region a:4-53 [148141]
2. YhbC-like, C-terminal domain [74942] (1)
   uperfamily
   1. YhbC-like, C-terminal domain [74943] (1)
      1. Hypothetical protein SP14.3 (SP0552) [74944]
         1. Streptococcus pneumoniae [TaxId: 1313] [74945] (1)
            1. 1ib8
               structural genomics
               1. region a:91-164 [71168]
3. GatD N-terminal domain-like [141300] (1)
   uperfamily
   1. GatD N-terminal domain-like [141301] (2)
      PfamB 010580
      1. Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD [141302]
         1. Pyrococcus abyssi [TaxId: 29292] [141303] (2)
            SQ Q9V0T9 2-75
            1. 1zq1
               complexed with asp
               1. region a:2-75 [125489]
            2. 1zq1
               automatically matched to 1ZQ1 A:2-75
               complexed with asp
               1. region b:2-75 [125491]
         2. Methanobacterium thermoautotrophicum [TaxId: 145262] [141304] (2)
            SQ O26802 2-73
            1. 2d6f
               complexed with zn
               1. region a:2-73 [131303]
            2. 2d6f
               automatically matched to 2D6F A:2-73
               complexed with zn
               1. region b:2-73 [131305]
4. Dom34/Pelota N-terminal domain-like [159065] (1)
   1. Dom34/Pelota N-terminal domain-like [159066] (2)
      Warning: Pfam incorrectly assigns this domain to the same family as the structurally unrelated N-terminal domain of eRF1 (Pfam 03463)
      1. Cell division protein pelota [159067]
         1. Thermoplasma acidophilum [TaxId: 2303] [159068] (1)
            SQ Q9HJ74 1-126
            1. 2qi2
               1. region a:1-126 [150800]
      2. Dom34 [159069]
         1. Saccharomyces cerevisiae [TaxId: 4932] [159070] (3)
            SQ P33309 1-135
            1. 2vgn
               automatically matched to 2VGM A:1-135
               complexed with gol, po4
               1. region a:1-135 [153040]
            2. 2vgn
               automatically matched to 2VGM A:1-135
               complexed with gol, po4
               1. region b:1-135 [153043]
            3. 2vgm
               1. region a:1-135 [153037]
5. TrmB C-terminal domain-like [159071] (1)
   sugar-binding domain; permuted OB-fold?
   1. TrmB C-terminal domain-like [159072] (1)
      C-terminal part of PfamB 004822
      1. Transcriptional regulator TrmB [159073]
         1. Thermococcus litoralis [TaxId: 2265] [159074] (1)
            SQ Q7LYW4 247-338
            1. 2f5t
               complexed with imd, mal
               1. region x:247-338 [146996]

Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009 Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk