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

  1. Root: SCOPe 2.07
  2. 2344607Class b: All beta proteins [48724] (178 folds)
  3. 2381452Fold b.40: OB-fold [50198] (17 superfamilies)
    barrel, closed or partly opened n=5, S=10 or S=8; greek-key
  4. 2382744Superfamily b.40.4: Nucleic acid-binding proteins [50249] (18 families) (S)
  5. 2383132Family b.40.4.5: Cold shock DNA-binding domain-like [50282] (32 protein domains)
    barrel, closed; n=5, S=8

Protein Domains:

  1. 2383133Archaeal initiation factor-1a, aIF1a [63772] (1 species)
    evolutionary link between IF1 and eIF1a
  2. 2383136C-terminal domain of eIF5a homologue (Hex1) [82105] (1 species)
  3. 2383139C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296] (5 species)
    1. 2383140Species Leishmania infantum [TaxId:5671] [110195] (1 PDB entry)
      Uniprot Q9N9V6
    2. 2383142Species Methanococcus jannaschii [TaxId:2190] [50297] (2 PDB entries)
    3. 2383145Species Pyrobaculum aerophilum [TaxId:13773] [50298] (1 PDB entry)
    4. 2383147Species Pyrococcus horikoshii [TaxId:53953] [82104] (1 PDB entry)
    5. 2383151Species Trypanosome (Leishmania mexicana) [TaxId:5665] [117196] (1 PDB entry)
      Uniprot Q9N9V6 97% sequence identity
  4. 2383153C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670] (3 species)
    1. 2383154Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [117195] (6 PDB entries)
      Uniprot P34087
    2. 2383163Species Human (Homo sapiens) [TaxId:9606] [141309] (1 PDB entry)
      Uniprot P62487 78-171
    3. 2383168Species Methanococcus jannaschii [TaxId:2190] [88671] (1 PDB entry)
  5. 2383171Cold shock domain protein E1 (UNR) [117198] (1 species)
  6. 2383174Elongation factor P middle and C-terminal domains [110196] (1 species)
    duplication: contains two domains of this fold
  7. 2383180Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950] (3 species)
    1. 2383181Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [101764] (1 PDB entry)
    2. 2383183Species Human (Homo sapiens) [TaxId:9606] [74951] (2 PDB entries)
      Uniprot P05198
    3. 2383186Species Sulfolobus solfataricus [TaxId:2287] [141310] (2 PDB entries)
      Uniprot Q97Z79 1-84
  8. 2383192Exoribonuclease 2, RNB [159089] (1 species)
    RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain
  9. 2383212Exosome 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. 2383217Exosome component 1, EXOSC1 [159098] (1 species)
    3'-5' exoribonuclease CSL4 homolog
  11. 2383220Major cold shock protein [50283] (4 species)
    1. 2383221Species Bacillus caldolyticus [TaxId:1394] [50286] (8 PDB entries)
    2. 2383238Species Bacillus subtilis [TaxId:1423] [50285] (10 PDB entries)
    3. 2383251Species Escherichia coli [TaxId:562] [50284] (3 PDB entries)
    4. 2383255Species Thermotoga maritima [TaxId:2336] [69262] (1 PDB entry)
  12. 2383257N-terminal domain of ribosomal protein L2 [50299] (5 species)
    incomplete OB-fold lacking the last strand
    1. 2383258Species Bacillus stearothermophilus [TaxId:1422] [50300] (1 PDB entry)
    2. 2383261Species Deinococcus radiodurans [TaxId:1299] [159085] (5 PDB entries)
      Uniprot Q9RXJ9 33-127
    3. 2383267Species Escherichia coli [TaxId:562] [159086] (27 PDB entries)
      Uniprot P60422 3-124
    4. 2383295Species Haloarcula marismortui [TaxId:2238] [50301] (40 PDB entries)
      Uniprot P20276
      includes the N-terminal tail
    5. 2383336Species Thermus thermophilus [TaxId:274] [159084] (6 PDB entries)
      Uniprot Q72I07 1-125
  13. 2383343Probable GTPase EngC (YjeQ), N-terminal domain [110200] (2 species)
    1. 2383344Species Bacillus subtilis [TaxId:1423] [117197] (1 PDB entry)
      Uniprot O34530
    2. 2383346Species Thermotoga maritima [TaxId:2336] [110201] (1 PDB entry)
      Uniprot Q9X242 # TM1717
  14. 2383350Rho termination factor, RNA-binding domain [68910] (1 species)
  15. 2383389Ribonuclease II family protein DR0020 [159094] (1 species)
  16. 2383395Ribosomal protein S12 [50302] (2 species)
    1. 2383396Species Escherichia coli [TaxId:562] [159087] (25 PDB entries)
      Uniprot P0A7S3 1-123
    2. 2383422Species Thermus thermophilus [TaxId:274] [50303] (36 PDB entries)
      Uniprot P17293
  17. 2383459Ribosomal protein S17 [50304] (3 species)
    1. 2383460Species Bacillus stearothermophilus [TaxId:1422] [50306] (1 PDB entry)
    2. 2383462Species Escherichia coli [TaxId:562] [159088] (26 PDB entries)
      Uniprot P02373 3-82
    3. 2383489Species Thermus thermophilus [TaxId:274] [50305] (45 PDB entries)
      Uniprot P24321
  18. 2383535Ribosomal protein S28e [101765] (2 species)
    incomplete OB-fold lacking the last strand
    1. 2383536Species Methanobacterium thermoautotrophicum [TaxId:145262] [101767] (1 PDB entry)
    2. 2383538Species Pyrococcus horikoshii [TaxId:53953] [101766] (1 PDB entry)
  19. 2383540RNA polymerase I subunit A43, C-terminal domain [346050] (1 species)
  20. 2383546S1 domain of NusA [69265] (2 species)
    1. 2383547Species Mycobacterium tuberculosis [TaxId:1773] [69267] (3 PDB entries)
    2. 2383553Species Thermotoga maritima [TaxId:2336] [69266] (2 PDB entries)
  21. 2383556S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287] (2 species)
    1. 2383557Species Escherichia coli [TaxId:562] [50288] (1 PDB entry)
    2. 2383559Species Streptomyces antibioticus [TaxId:1890] [50289] (1 PDB entry)
  22. 2383561S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100] (3 species)
    1. 2383562Species Aeropyrum pernix [TaxId:56636] [159101] (1 PDB entry)
      Uniprot Q9YC02 60-147
    2. 2383564Species Archaeoglobus fulgidus [TaxId:2234] [159103] (1 PDB entry)
      Uniprot O29758 53-135
    3. 2383568Species Sulfolobus solfataricus [TaxId:2287] [159102] (4 PDB entries)
      Uniprot Q9UXC4 66-152
  23. 2383573S1-domain of exosome component 3 (RRP40) [159091] (2 species)
    1. 2383574Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [159092] (1 PDB entry)
      Uniprot Q08285 62-151
    2. 2383576Species Human (Homo sapiens) [TaxId:9606] [159093] (1 PDB entry)
      Uniprot Q9NQT5 108-195
  24. 2383578S1-domain of Ribonuclease E [110198] (1 species)
  25. 2383585S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096] (1 species)
  26. 2383588S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200] (1 species)
  27. 2383591Tex S1-domain [159106] (1 species)
  28. 2383596Translation initiation factor-1a, eIF1a [50292] (1 species)
  29. 2383599Translational initiation factor 1, IF1 [50290] (1 species)
  30. 2383604Viral structural mimic of eIF2alpha [74952] (2 species)
    1. 2383605Species Myxoma virus, m156r [TaxId:10273] [74954] (1 PDB entry)
    2. 2383607Species Vaccinia virus [TaxId:10245] [74953] (1 PDB entry)
  31. 2383610Y-box protein 1 cold shock domain (YB1-CSD) [69263] (1 species)
  32. 2383613automated matches [190915] (10 species)
    not a true protein
    1. 2383614Species Burkholderia thailandensis [TaxId:271848] [274220] (1 PDB entry)
    2. 2383616Species Listeria monocytogenes [TaxId:169963] [311222] (2 PDB entries)
    3. 2383619Species Mycobacterium tuberculosis [TaxId:83332] [189240] (1 PDB entry)
    4. 2383622Species Neisseria meningitidis [TaxId:122586] [188390] (1 PDB entry)
    5. 2383625Species Pseudomonas aeruginosa [TaxId:287] [322282] (1 PDB entry)
    6. 2383627Species Salmonella typhimurium [TaxId:90371] [189151] (1 PDB entry)
    7. 2383630Species Staphylococcus aureus [TaxId:158878] [324536] (1 PDB entry)
    8. 2383632Species Streptococcus pneumoniae [TaxId:170187] [258407] (1 PDB entry)
    9. 2383635Species Thermus aquaticus [TaxId:498848] [311225] (2 PDB entries)
    10. 2383638Species 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: