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

  1. Root: SCOPe 2.01
  2. 929298Class b: All beta proteins [48724] (174 folds)
  3. 949212Fold b.40: OB-fold [50198] (16 superfamilies)
    barrel, closed or partly opened n=5, S=10 or S=8; greek-key
  4. 950107Superfamily b.40.4: Nucleic acid-binding proteins [50249] (17 families) (S)
  5. 950437Family b.40.4.5: Cold shock DNA-binding domain-like [50282] (31 proteins)
    barrel, closed; n=5, S=8

Proteins:

  1. 950438Archaeal initiation factor-1a, aIF1a [63772] (1 species)
    evolutionary link between IF1 and eIF1a
  2. 950441C-terminal domain of eIF5a homologue (Hex1) [82105] (1 species)
  3. 950444C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296] (5 species)
    1. 950445Species Leishmania infantum [TaxId:5671] [110195] (1 PDB entry)
      Uniprot Q9N9V6
    2. 950447Species Methanococcus jannaschii [TaxId:2190] [50297] (2 PDB entries)
    3. 950450Species Pyrobaculum aerophilum [TaxId:13773] [50298] (1 PDB entry)
    4. 950452Species Pyrococcus horikoshii [TaxId:53953] [82104] (1 PDB entry)
    5. 950456Species Trypanosome (Leishmania mexicana) [TaxId:5665] [117196] (1 PDB entry)
      Uniprot Q9N9V6 97% sequence identity
  4. 950458C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670] (3 species)
    1. 950459Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [117195] (6 PDB entries)
      Uniprot P34087
    2. 950468Species Human (Homo sapiens) [TaxId:9606] [141309] (1 PDB entry)
      Uniprot P62487 78-171
    3. 950473Species Methanococcus jannaschii [TaxId:2190] [88671] (1 PDB entry)
  5. 950476Cold shock domain protein E1 (UNR) [117198] (1 species)
  6. 950479Elongation factor P middle and C-terminal domains [110196] (1 species)
    duplication: contains two domains of this fold
  7. 950485Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950] (3 species)
    1. 950486Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [101764] (1 PDB entry)
    2. 950488Species Human (Homo sapiens) [TaxId:9606] [74951] (2 PDB entries)
      Uniprot P05198
    3. 950491Species Sulfolobus solfataricus [TaxId:2287] [141310] (1 PDB entry)
      Uniprot Q97Z79 1-84
  8. 950493Exoribonuclease 2, RNB [159089] (1 species)
    RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain
  9. 950513Exosome 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. 950518Exosome component 1, EXOSC1 [159098] (1 species)
    3'-5' exoribonuclease CSL4 homolog
  11. 950521Major cold shock protein [50283] (4 species)
    1. 950522Species Bacillus caldolyticus [TaxId:1394] [50286] (7 PDB entries)
    2. 950537Species Bacillus subtilis [TaxId:1423] [50285] (10 PDB entries)
    3. 950550Species Escherichia coli [TaxId:562] [50284] (2 PDB entries)
    4. 950553Species Thermotoga maritima [TaxId:2336] [69262] (1 PDB entry)
  12. 950555N-terminal domain of ribosomal protein L2 [50299] (5 species)
    incomplete OB-fold lacking the last strand
    1. 950556Species Bacillus stearothermophilus [TaxId:1422] [50300] (2 PDB entries)
    2. 950560Species Deinococcus radiodurans [TaxId:1299] [159085] (5 PDB entries)
      Uniprot Q9RXJ9 33-127
    3. 950566Species Escherichia coli [TaxId:562] [159086] (27 PDB entries)
      Uniprot P60422 3-124
    4. 950594Species Haloarcula marismortui [TaxId:2238] [50301] (40 PDB entries)
      Uniprot P20276
      includes the N-terminal tail
    5. 950635Species Thermus thermophilus [TaxId:274] [159084] (5 PDB entries)
      Uniprot Q72I07 1-125
  13. 950641Probable GTPase EngC (YjeQ), N-terminal domain [110200] (2 species)
    1. 950642Species Bacillus subtilis [TaxId:1423] [117197] (1 PDB entry)
      Uniprot O34530
    2. 950644Species Thermotoga maritima [TaxId:2336] [110201] (1 PDB entry)
      Uniprot Q9X242 # TM1717
  14. 950648Rho termination factor, RNA-binding domain [68910] (1 species)
  15. 950687Ribonuclease II family protein DR0020 [159094] (1 species)
  16. 950693Ribosomal protein S12 [50302] (2 species)
    1. 950694Species Escherichia coli [TaxId:562] [159087] (25 PDB entries)
      Uniprot P0A7S3 1-123
    2. 950720Species Thermus thermophilus [TaxId:274] [50303] (36 PDB entries)
      Uniprot P17293
  17. 950757Ribosomal protein S17 [50304] (3 species)
    1. 950758Species Bacillus stearothermophilus [TaxId:1422] [50306] (1 PDB entry)
    2. 950760Species Escherichia coli [TaxId:562] [159088] (26 PDB entries)
      Uniprot P02373 3-82
    3. 950787Species Thermus thermophilus [TaxId:274] [50305] (45 PDB entries)
      Uniprot P24321
  18. 950833Ribosomal protein S28e [101765] (2 species)
    incomplete OB-fold lacking the last strand
    1. 950834Species Methanobacterium thermoautotrophicum [TaxId:145262] [101767] (1 PDB entry)
    2. 950836Species Pyrococcus horikoshii [TaxId:53953] [101766] (1 PDB entry)
  19. 950838S1 domain of NusA [69265] (2 species)
    1. 950839Species Mycobacterium tuberculosis [TaxId:1773] [69267] (3 PDB entries)
    2. 950845Species Thermotoga maritima [TaxId:2336] [69266] (2 PDB entries)
  20. 950848S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287] (2 species)
    1. 950849Species Escherichia coli [TaxId:562] [50288] (1 PDB entry)
    2. 950851Species Streptomyces antibioticus [TaxId:1890] [50289] (1 PDB entry)
  21. 950853S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100] (3 species)
    1. 950854Species Aeropyrum pernix [TaxId:56636] [159101] (1 PDB entry)
      Uniprot Q9YC02 60-147
    2. 950856Species Archaeoglobus fulgidus [TaxId:2234] [159103] (1 PDB entry)
      Uniprot O29758 53-135
    3. 950860Species Sulfolobus solfataricus [TaxId:2287] [159102] (2 PDB entries)
      Uniprot Q9UXC4 66-152
  22. 950863S1-domain of exosome component 3 (RRP40) [159091] (2 species)
    1. 950864Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [159092] (1 PDB entry)
      Uniprot Q08285 62-151
    2. 950866Species Human (Homo sapiens) [TaxId:9606] [159093] (1 PDB entry)
      Uniprot Q9NQT5 108-195
  23. 950868S1-domain of Ribonuclease E [110198] (1 species)
  24. 950875S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096] (1 species)
  25. 950878S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200] (1 species)
  26. 950881Tex S1-domain [159106] (1 species)
  27. 950886Translation initiation factor-1a, eIF1a [50292] (1 species)
  28. 950889Translational initiation factor 1, IF1 [50290] (1 species)
  29. 950894Viral structural mimic of eIF2alpha [74952] (2 species)
    1. 950895Species Myxoma virus, m156r [TaxId:10273] [74954] (1 PDB entry)
    2. 950897Species Vaccinia virus [TaxId:10245] [74953] (1 PDB entry)
  30. 950900Y-box protein 1 cold shock domain (YB1-CSD) [69263] (1 species)
  31. 950903automated matches [190915] (4 species)
    not a true protein
    1. 950904Species Mycobacterium tuberculosis [TaxId:83332] [189240] (1 PDB entry)
    2. 950907Species Neisseria meningitidis [TaxId:122586] [188390] (1 PDB entry)
    3. 950910Species Salmonella typhimurium [TaxId:90371] [189151] (1 PDB entry)
    4. 950913Species 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: