Structural Classification of Proteins
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Family: Cold shock DNA-binding domain-like

barrel, closed; n=5, S=8

Lineage:

  1. Root: scop
  2. Class: All beta proteins [48724]
  3. Fold: OB-fold [50198]
    barrel, closed or partly opened n=5, S=10 or S=8; greek-key
  4. Superfamily: Nucleic acid-binding proteins [50249]
    link to SUPERFAMILY database - Superfamily
  5. Family: Cold shock DNA-binding domain-like [50282]
    barrel, closed; n=5, S=8

Protein Domains:

  1. Major cold shock protein [50283]
    1. Escherichia coli [TaxId: 562] [50284] (2) picpic
    2. Bacillus subtilis [TaxId: 1423] [50285] (6) picpic
    3. Bacillus caldolyticus [TaxId: 1394] [50286] (8) picpic
    4. Thermotoga maritima [TaxId: 2336] [69262] (1) picpic
  2. Y-box protein 1 cold shock domain (YB1-CSD) [69263]
    1. Human (Homo sapiens) [TaxId: 9606] [69264] (1) picpic
  3. S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287]
    1. Escherichia coli [TaxId: 562] [50288] (1) picpic
    2. Streptomyces antibioticus [TaxId: 1890] [50289] (1) picpic
  4. S1 domain of NusA [69265]
    1. Thermotoga maritima [TaxId: 2336] [69266] (2) picpic
    2. Mycobacterium tuberculosis [TaxId: 1773] [69267] (4) picpic
  5. C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670]
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [88671] (1) picpic
    2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117195] (7) picpic
      SQ P34087
    3. Human (Homo sapiens) [TaxId: 9606] [141309] (4) picpic
      SQ P62487 78-171
  6. Translational initiation factor 1, IF1 [50290]
    1. Escherichia coli [TaxId: 562] [50291] (3) picpic
  7. Archaeal initiation factor-1a, aIF1a [63772]
    evolutionary link between IF1 and eIF1a
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [63773] (1) picpic
  8. Translation initiation factor-1a, eIF1a [50292]
    1. Human (Homo sapiens) [TaxId: 9606] [50293] (1) picpic
  9. Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950]
    1. Human (Homo sapiens) [TaxId: 9606] [74951] (2) picpic
      SQ P05198
    2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101764] (1) picpic
    3. Sulfolobus solfataricus [TaxId: 2287] [141310] (1) picpic
      SQ Q97Z79 1-84
  10. Viral structural mimic of eIF2alpha [74952]
    1. Vaccinia virus [TaxId: 10245] [74953] (1) picpic
    2. Myxoma virus, m156r [TaxId: 10273] [74954] (1) picpic
  11. Rho termination factor, RNA-binding domain [68910]
    1. Escherichia coli [TaxId: 562] [68911] (14) picpic
      SQ P03002
  12. C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296]
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [50297] (2) picpic
    2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [50298] (1) picpic
    3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82104] (1) picpic
    4. Leishmania infantum [TaxId: 5671] [110195] (1) picpic
      SQ Q9N9V6
    5. Leishmania mexicana [TaxId: 5665] [117196] (1) picpic
      SQ Q9N9V6 97% sequence identity
  13. C-terminal domain of eIF5a homologue (Hex1) [82105]
    1. Filamentous fungi (Neurospora crassa) [TaxId: 5141] [82106] (1) picpic
  14. N-terminal domain of ribosomal protein L2 [50299]
    incomplete OB-fold lacking the last strand
    1. Bacillus stearothermophilus [TaxId: 1422] [50300] (2) picpic
    2. Archaeon Haloarcula marismortui [TaxId: 2238] [50301] (40) picpic
      SQ P20276
      includes the N-terminal tail
    3. Thermus thermophilus [TaxId: 274] [159084] (5) picpic
      SQ Q72I07 1-125
    4. Deinococcus radiodurans [TaxId: 1299] [159085] (5) picpic
      SQ Q9RXJ9 33-127
    5. Escherichia coli [TaxId: 562] [159086] (27) picpic
      SQ P60422 3-124
  15. Ribosomal protein S12 [50302]
    1. Thermus thermophilus [TaxId: 274] [50303] (36) picpic
      SQ P17293
    2. Escherichia coli [TaxId: 562] [159087] (25) picpic
      SQ P0A7S3 1-123
  16. Ribosomal protein S17 [50304]
    1. Thermus thermophilus [TaxId: 274] [50305] (45) picpic
      SQ P24321
    2. Bacillus stearothermophilus [TaxId: 1422] [50306] (1) picpic
    3. Escherichia coli [TaxId: 562] [159088] (26) picpic
      SQ P02373 3-82
  17. Ribosomal protein S28e [101765]
    incomplete OB-fold lacking the last strand
    1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101766] (1) picpic
    2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101767] (1) picpic
  18. Elongation factor P middle and C-terminal domains [110196]
    duplication: contains two domains of this fold
    1. Thermus thermophilus HB8 [TaxId: 300852] [110197] (1) picpic
      SQ Q76G20
  19. S1-domain of Ribonuclease E [110198]
    1. Escherichia coli [TaxId: 562] [110199] (3) picpic
      SQ P21513 35-125
  20. Probable GTPase EngC (YjeQ), N-terminal domain [110200]
    1. Thermotoga maritima [TaxId: 2336] [110201] (1) picpic
      SQ Q9X242 # TM1717
    2. Bacillus subtilis [TaxId: 1423] [117197] (1) picpic
      SQ O34530
  21. Cold shock domain protein E1 (UNR) [117198]
    1. Human (Homo sapiens) [TaxId: 9606] [117199] (1) picpic
      SQ O75534 15-90
  22. S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200]
    1. Human (Homo sapiens) [TaxId: 9606] [117201] (1) picpic
      SQ Q14690 173-278
  23. Exoribonuclease 2, RNB [159089]
    RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain
    1. Escherichia coli [TaxId: 562] [159090] (18) picpic
      SQ P30850 1-82! SQ P30850 4-82! SQ P30850 5-82! SQ P30850 558-643! SQ P30850 558-644! SQ P30850 83-172
  24. S1-domain of exosome component 3 (RRP40) [159091]
    1. Saccharomyces cerevisiae [TaxId: 4932] [159092] (1) picpic
      SQ Q08285 62-151
    2. Human (Homo sapiens) [TaxId: 9606] [159093] (1) picpic
      SQ Q9NQT5 108-195
  25. Ribonuclease II family protein DR0020 [159094]
    1. Deinococcus radiodurans [TaxId: 1299] [159095] (4) picpic
      SQ Q9RYD0 404-461
  26. S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096]
    1. Human (Homo sapiens) [TaxId: 9606] [159097] (1) picpic
      SQ Q13868 73-167
  27. Exosome component 1, EXOSC1 [159098]
    3'-5' exoribonuclease CSL4 homolog
    1. Human (Homo sapiens) [TaxId: 9606] [159099] (1) picpic
      SQ Q9Y3B2 61-185
  28. S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100]
    1. Aeropyrum pernix [TaxId: 56636] [159101] (1) picpic
      SQ Q9YC02 60-147
    2. Sulfolobus solfataricus [TaxId: 2287] [159102] (2) picpic
      SQ Q9UXC4 66-152
    3. Archaeoglobus fulgidus [TaxId: 2234] [159103] (3) picpic
      SQ O29758 53-135
  29. Exosome complex exonuclease RRP44 [159104]
    member or the RNase II family; contains 3 S1-like domains; two of them are in tandem N-terminally to the catalytic domain and one is C-terminally to the catalytic domain that also contains an OB-fold
    1. Saccharomyces cerevisiae [TaxId: 4932] [159105] (3) picpic
      SQ Q08162 252-399! SQ Q08162 400-494! SQ Q08162 911-998
  30. Tex S1-domain [159106]
    1. Pseudomonas aeruginosa [TaxId: 287] [159107] (3) picpic
      SQ Q9HTY8 637-730
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MRC site 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