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

  1. Root: SCOPe 2.03
  2. 1287432Class b: All beta proteins [48724] (174 folds)
  3. 1313473Fold b.40: OB-fold [50198] (16 superfamilies)
    barrel, closed or partly opened n=5, S=10 or S=8; greek-key
  4. 1314543Superfamily b.40.4: Nucleic acid-binding proteins [50249] (17 families) (S)
  5. 1314898Family b.40.4.5: Cold shock DNA-binding domain-like [50282] (31 proteins)
    barrel, closed; n=5, S=8

Proteins:

  1. 1314899Archaeal initiation factor-1a, aIF1a [63772] (1 species)
    evolutionary link between IF1 and eIF1a
  2. 1314902C-terminal domain of eIF5a homologue (Hex1) [82105] (1 species)
  3. 1314905C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296] (5 species)
    1. 1314906Species Leishmania infantum [TaxId:5671] [110195] (1 PDB entry)
      Uniprot Q9N9V6
    2. 1314908Species Methanococcus jannaschii [TaxId:2190] [50297] (2 PDB entries)
    3. 1314911Species Pyrobaculum aerophilum [TaxId:13773] [50298] (1 PDB entry)
    4. 1314913Species Pyrococcus horikoshii [TaxId:53953] [82104] (1 PDB entry)
    5. 1314917Species Trypanosome (Leishmania mexicana) [TaxId:5665] [117196] (1 PDB entry)
      Uniprot Q9N9V6 97% sequence identity
  4. 1314919C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670] (3 species)
    1. 1314920Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [117195] (6 PDB entries)
      Uniprot P34087
    2. 1314929Species Human (Homo sapiens) [TaxId:9606] [141309] (1 PDB entry)
      Uniprot P62487 78-171
    3. 1314934Species Methanococcus jannaschii [TaxId:2190] [88671] (1 PDB entry)
  5. 1314937Cold shock domain protein E1 (UNR) [117198] (1 species)
  6. 1314940Elongation factor P middle and C-terminal domains [110196] (1 species)
    duplication: contains two domains of this fold
  7. 1314946Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950] (3 species)
    1. 1314947Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [101764] (1 PDB entry)
    2. 1314949Species Human (Homo sapiens) [TaxId:9606] [74951] (2 PDB entries)
      Uniprot P05198
    3. 1314952Species Sulfolobus solfataricus [TaxId:2287] [141310] (2 PDB entries)
      Uniprot Q97Z79 1-84
  8. 1314958Exoribonuclease 2, RNB [159089] (1 species)
    RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain
  9. 1314978Exosome 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
  10. 1314983Exosome component 1, EXOSC1 [159098] (1 species)
    3'-5' exoribonuclease CSL4 homolog
  11. 1314986Major cold shock protein [50283] (4 species)
    1. 1314987Species Bacillus caldolyticus [TaxId:1394] [50286] (7 PDB entries)
    2. 1315002Species Bacillus subtilis [TaxId:1423] [50285] (10 PDB entries)
    3. 1315015Species Escherichia coli [TaxId:562] [50284] (2 PDB entries)
    4. 1315018Species Thermotoga maritima [TaxId:2336] [69262] (1 PDB entry)
  12. 1315020N-terminal domain of ribosomal protein L2 [50299] (5 species)
    incomplete OB-fold lacking the last strand
    1. 1315021Species Bacillus stearothermophilus [TaxId:1422] [50300] (1 PDB entry)
    2. 1315024Species Deinococcus radiodurans [TaxId:1299] [159085] (5 PDB entries)
      Uniprot Q9RXJ9 33-127
    3. 1315030Species Escherichia coli [TaxId:562] [159086] (27 PDB entries)
      Uniprot P60422 3-124
    4. 1315058Species Haloarcula marismortui [TaxId:2238] [50301] (40 PDB entries)
      Uniprot P20276
      includes the N-terminal tail
    5. 1315099Species Thermus thermophilus [TaxId:274] [159084] (6 PDB entries)
      Uniprot Q72I07 1-125
  13. 1315106Probable GTPase EngC (YjeQ), N-terminal domain [110200] (2 species)
    1. 1315107Species Bacillus subtilis [TaxId:1423] [117197] (1 PDB entry)
      Uniprot O34530
    2. 1315109Species Thermotoga maritima [TaxId:2336] [110201] (1 PDB entry)
      Uniprot Q9X242 # TM1717
  14. 1315113Rho termination factor, RNA-binding domain [68910] (1 species)
  15. 1315152Ribonuclease II family protein DR0020 [159094] (1 species)
  16. 1315158Ribosomal protein S12 [50302] (2 species)
    1. 1315159Species Escherichia coli [TaxId:562] [159087] (25 PDB entries)
      Uniprot P0A7S3 1-123
    2. 1315185Species Thermus thermophilus [TaxId:274] [50303] (36 PDB entries)
      Uniprot P17293
  17. 1315222Ribosomal protein S17 [50304] (3 species)
    1. 1315223Species Bacillus stearothermophilus [TaxId:1422] [50306] (1 PDB entry)
    2. 1315225Species Escherichia coli [TaxId:562] [159088] (26 PDB entries)
      Uniprot P02373 3-82
    3. 1315252Species Thermus thermophilus [TaxId:274] [50305] (45 PDB entries)
      Uniprot P24321
  18. 1315298Ribosomal protein S28e [101765] (2 species)
    incomplete OB-fold lacking the last strand
    1. 1315299Species Methanobacterium thermoautotrophicum [TaxId:145262] [101767] (1 PDB entry)
    2. 1315301Species Pyrococcus horikoshii [TaxId:53953] [101766] (1 PDB entry)
  19. 1315303S1 domain of NusA [69265] (2 species)
    1. 1315304Species Mycobacterium tuberculosis [TaxId:1773] [69267] (3 PDB entries)
    2. 1315310Species Thermotoga maritima [TaxId:2336] [69266] (2 PDB entries)
  20. 1315313S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287] (2 species)
    1. 1315314Species Escherichia coli [TaxId:562] [50288] (1 PDB entry)
    2. 1315316Species Streptomyces antibioticus [TaxId:1890] [50289] (1 PDB entry)
  21. 1315318S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100] (3 species)
    1. 1315319Species Aeropyrum pernix [TaxId:56636] [159101] (1 PDB entry)
      Uniprot Q9YC02 60-147
    2. 1315321Species Archaeoglobus fulgidus [TaxId:2234] [159103] (1 PDB entry)
      Uniprot O29758 53-135
    3. 1315325Species Sulfolobus solfataricus [TaxId:2287] [159102] (4 PDB entries)
      Uniprot Q9UXC4 66-152
  22. 1315330S1-domain of exosome component 3 (RRP40) [159091] (2 species)
    1. 1315331Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [159092] (1 PDB entry)
      Uniprot Q08285 62-151
    2. 1315333Species Human (Homo sapiens) [TaxId:9606] [159093] (1 PDB entry)
      Uniprot Q9NQT5 108-195
  23. 1315335S1-domain of Ribonuclease E [110198] (1 species)
  24. 1315342S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096] (1 species)
  25. 1315345S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200] (1 species)
  26. 1315348Tex S1-domain [159106] (1 species)
  27. 1315353Translation initiation factor-1a, eIF1a [50292] (1 species)
  28. 1315356Translational initiation factor 1, IF1 [50290] (1 species)
  29. 1315361Viral structural mimic of eIF2alpha [74952] (2 species)
    1. 1315362Species Myxoma virus, m156r [TaxId:10273] [74954] (1 PDB entry)
    2. 1315364Species Vaccinia virus [TaxId:10245] [74953] (1 PDB entry)
  30. 1315367Y-box protein 1 cold shock domain (YB1-CSD) [69263] (1 species)
  31. 1315370automated matches [190915] (4 species)
    not a true protein
    1. 1315371Species Mycobacterium tuberculosis [TaxId:83332] [189240] (1 PDB entry)
    2. 1315374Species Neisseria meningitidis [TaxId:122586] [188390] (1 PDB entry)
    3. 1315377Species Salmonella typhimurium [TaxId:90371] [189151] (1 PDB entry)
    4. 1315380Species Thermus thermophilus [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: