SCOPe 2.07: Family b.40.4.5: Cold shock DNA-binding domain-like

Lineage for Family b.40.4.5: Cold shock DNA-binding domain-like

1. Root: SCOPe 2.07

2. Class b: All beta proteins [48724] (178 folds)

3. Fold b.40: OB-fold [50198] (17 superfamilies)
   barrel, closed or partly opened n=5, S=10 or S=8; greek-key

4. Superfamily b.40.4: Nucleic acid-binding proteins [50249] (18 families)

5. Family b.40.4.5: Cold shock DNA-binding domain-like [50282] (32 proteins)
   barrel, closed; n=5, S=8

Proteins:

1. Archaeal initiation factor-1a, aIF1a [63772] (1 species)
   evolutionary link between IF1 and eIF1a

   • Species Methanococcus jannaschii [TaxId:2190] [63773] (1 PDB entry)

2. C-terminal domain of eIF5a homologue (Hex1) [82105] (2 species)

   1. Species Fungus (Neurospora crassa) [TaxId:5141] [82106] (1 PDB entry)

   2. Species Neurospora crassa [TaxId:367110] [405798] (2 PDB entries)

3. C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296] (5 species)

   1. Species Leishmania infantum [TaxId:5671] [110195] (1 PDB entry)
      Uniprot Q9N9V6

   2. Species Methanococcus jannaschii [TaxId:2190] [50297] (2 PDB entries)

   3. Species Pyrobaculum aerophilum [TaxId:13773] [50298] (1 PDB entry)

   4. Species Pyrococcus horikoshii [TaxId:53953] [82104] (1 PDB entry)

   5. Species Trypanosome (Leishmania mexicana) [TaxId:5665] [117196] (1 PDB entry)
      Uniprot Q9N9V6 97% sequence identity

4. C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670] (3 species)

   1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [117195] (6 PDB entries)
      Uniprot P34087

   2. Species Human (Homo sapiens) [TaxId:9606] [141309] (1 PDB entry)
      Uniprot P62487 78-171

   3. Species Methanococcus jannaschii [TaxId:2190] [88671] (1 PDB entry)

5. Cold shock domain protein E1 (UNR) [117198] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117199] (1 PDB entry)
     Uniprot O75534 15-90

6. Elongation factor P middle and C-terminal domains [110196] (1 species)
   duplication: contains two domains of this fold

   • Species Thermus thermophilus HB8 [TaxId:300852] [110197] (1 PDB entry)
     Uniprot Q76G20

7. Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950] (3 species)

   1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [101764] (1 PDB entry)

   2. Species Human (Homo sapiens) [TaxId:9606] [74951] (2 PDB entries)
      Uniprot P05198

   3. Species Sulfolobus solfataricus [TaxId:2287] [141310] (2 PDB entries)
      Uniprot Q97Z79 1-84

8. Exoribonuclease 2, RNB [159089] (1 species)
   RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain

   • Species Escherichia coli [TaxId:562] [159090] (3 PDB entries)
     Uniprot P30850 1-82! Uniprot P30850 4-82! Uniprot P30850 5-82! Uniprot P30850 558-643! Uniprot P30850 558-644! Uniprot P30850 83-172

9. Exosome complex exonuclease RRP44 [159104] (1 species)
   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

   • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [159105] (1 PDB entry)
     Uniprot Q08162 252-399! Uniprot Q08162 400-494! Uniprot Q08162 911-998

10. Exosome component 1, EXOSC1 [159098] (1 species)
    3'-5' exoribonuclease CSL4 homolog

    • Species Human (Homo sapiens) [TaxId:9606] [159099] (1 PDB entry)
      Uniprot Q9Y3B2 61-185

11. Major cold shock protein [50283] (4 species)

    1. Species Bacillus caldolyticus [TaxId:1394] [50286] (8 PDB entries)

    2. Species Bacillus subtilis [TaxId:1423] [50285] (12 PDB entries)

    3. Species Escherichia coli [TaxId:562] [50284] (3 PDB entries)

    4. Species Thermotoga maritima [TaxId:2336] [69262] (1 PDB entry)

12. N-terminal domain of ribosomal protein L2 [50299] (5 species)
    incomplete OB-fold lacking the last strand

    1. Species Bacillus stearothermophilus [TaxId:1422] [50300] (1 PDB entry)

    2. Species Deinococcus radiodurans [TaxId:1299] [159085] (5 PDB entries)
       Uniprot Q9RXJ9 33-127

    3. Species Escherichia coli [TaxId:562] [159086] (27 PDB entries)
       Uniprot P60422 3-124

    4. Species Haloarcula marismortui [TaxId:2238] [50301] (40 PDB entries)
       Uniprot P20276
       includes the N-terminal tail

    5. Species Thermus thermophilus [TaxId:274] [159084] (6 PDB entries)
       Uniprot Q72I07 1-125

13. Probable GTPase EngC (YjeQ), N-terminal domain [110200] (2 species)

    1. Species Bacillus subtilis [TaxId:1423] [117197] (1 PDB entry)
       Uniprot O34530

    2. Species Thermotoga maritima [TaxId:2336] [110201] (1 PDB entry)
       Uniprot Q9X242 # TM1717

14. Rho termination factor, RNA-binding domain [68910] (1 species)

    • Species Escherichia coli [TaxId:562] [68911] (9 PDB entries)
      Uniprot P03002

15. Ribonuclease II family protein DR0020 [159094] (1 species)

    • Species Deinococcus radiodurans [TaxId:1299] [159095] (2 PDB entries)
      Uniprot Q9RYD0 404-461

16. Ribosomal protein S12 [50302] (2 species)

    1. Species Escherichia coli [TaxId:562] [159087] (25 PDB entries)
       Uniprot P0A7S3 1-123

    2. Species Thermus thermophilus [TaxId:274] [50303] (36 PDB entries)
       Uniprot P17293

17. Ribosomal protein S17 [50304] (3 species)

    1. Species Bacillus stearothermophilus [TaxId:1422] [50306] (1 PDB entry)

    2. Species Escherichia coli [TaxId:562] [159088] (26 PDB entries)
       Uniprot P02373 3-82

    3. Species Thermus thermophilus [TaxId:274] [50305] (45 PDB entries)
       Uniprot P24321

18. Ribosomal protein S28e [101765] (2 species)
    incomplete OB-fold lacking the last strand

    1. Species Methanobacterium thermoautotrophicum [TaxId:145262] [101767] (1 PDB entry)

    2. Species Pyrococcus horikoshii [TaxId:53953] [101766] (1 PDB entry)

19. RNA polymerase I subunit A43, C-terminal domain [346050] (1 species)

    • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [346240] (2 PDB entries)

20. S1 domain of NusA [69265] (2 species)

    1. Species Mycobacterium tuberculosis [TaxId:1773] [69267] (3 PDB entries)

    2. Species Thermotoga maritima [TaxId:2336] [69266] (2 PDB entries)

21. S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287] (2 species)

    1. Species Escherichia coli [TaxId:562] [50288] (1 PDB entry)

    2. Species Streptomyces antibioticus [TaxId:1890] [50289] (1 PDB entry)

22. S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100] (3 species)

    1. Species Aeropyrum pernix [TaxId:56636] [159101] (1 PDB entry)
       Uniprot Q9YC02 60-147

    2. Species Archaeoglobus fulgidus [TaxId:2234] [159103] (1 PDB entry)
       Uniprot O29758 53-135

    3. Species Sulfolobus solfataricus [TaxId:2287] [159102] (4 PDB entries)
       Uniprot Q9UXC4 66-152

23. S1-domain of exosome component 3 (RRP40) [159091] (2 species)

    1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [159092] (1 PDB entry)
       Uniprot Q08285 62-151

    2. Species Human (Homo sapiens) [TaxId:9606] [159093] (1 PDB entry)
       Uniprot Q9NQT5 108-195

24. S1-domain of Ribonuclease E [110198] (1 species)

    • Species Escherichia coli [TaxId:562] [110199] (3 PDB entries)
      Uniprot P21513 35-125

25. S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [159097] (1 PDB entry)
      Uniprot Q13868 73-167

26. S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117201] (1 PDB entry)
      Uniprot Q14690 173-278

27. Tex S1-domain [159106] (1 species)

    • Species Pseudomonas aeruginosa [TaxId:287] [159107] (3 PDB entries)
      Uniprot Q9HTY8 637-730

28. Translation initiation factor-1a, eIF1a [50292] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [50293] (1 PDB entry)

29. Translational initiation factor 1, IF1 [50290] (1 species)

    • Species Escherichia coli [TaxId:562] [50291] (3 PDB entries)

30. Viral structural mimic of eIF2alpha [74952] (2 species)

    1. Species Myxoma virus, m156r [TaxId:10273] [74954] (1 PDB entry)

    2. Species Vaccinia virus [TaxId:10245] [74953] (1 PDB entry)

31. Y-box protein 1 cold shock domain (YB1-CSD) [69263] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [69264] (1 PDB entry)

32. automated matches [190915] (12 species)
    not a true protein

    1. Species Burkholderia thailandensis [TaxId:271848] [274220] (1 PDB entry)

    2. Species Homo sapiens [TaxId:9606] [369483] (2 PDB entries)

    3. Species Listeria monocytogenes [TaxId:169963] [311222] (2 PDB entries)

    4. Species Mycobacterium tuberculosis [TaxId:83332] [189240] (1 PDB entry)

    5. Species Neisseria meningitidis [TaxId:122586] [188390] (1 PDB entry)

    6. Species Peptoclostridium difficile [TaxId:1496] [362011] (1 PDB entry)

    7. Species Pseudomonas aeruginosa [TaxId:287] [322282] (1 PDB entry)

    8. Species Salmonella typhimurium [TaxId:90371] [189151] (1 PDB entry)

    9. Species Staphylococcus aureus [TaxId:158878] [324536] (1 PDB entry)

    10. Species Streptococcus pneumoniae [TaxId:170187] [258407] (1 PDB entry)

    11. Species Thermus aquaticus [TaxId:498848] [311225] (2 PDB entries)

    12. Species Thermus thermophilus HB8 [TaxId:300852] [189282] (1 PDB entry)

More info for Family b.40.4.5: Cold shock DNA-binding domain-like

Timeline for Family b.40.4.5: Cold shock DNA-binding domain-like:

• Family b.40.4.5: Cold shock DNA-binding domain-like first appeared (with stable ids) in SCOP 1.55
  
• Family b.40.4.5: Cold shock DNA-binding domain-like appears in SCOPe 2.06
  
• Family b.40.4.5: Cold shock DNA-binding domain-like appears in the current release, SCOPe 2.08