SCOP 1.71: 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: SCOP 1.71

2. Class b: All beta proteins [48724] (149 folds)

3. Fold b.40: OB-fold [50198] (10 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] (13 families)

5. Family b.40.4.5: Cold shock DNA-binding domain-like [50282] (22 proteins)
   barrel, closed; n=5, S=8

Proteins:

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

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

2. C-terminal domain of eIF5a homologue (Hex1) [82105] (1 species)

   • Species Filamentous fungi (Neurospora crassa) [TaxId:5141] [82106] (1 PDB entry)

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

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

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

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

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

   5. Species Leishmania mexicana TaxID: 5665 [TaxId:5665] [117196] (1 PDB entry)

4. C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670] (2 species)

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

   2. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [117195] (1 PDB entry)

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

   • Species Human (Homo sapiens) [TaxId:9606] [117199] (1 PDB entry)

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)

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

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

   1. Species Bacillus caldolyticus [TaxId:1394] [50286] (6 PDB entries)

   2. Species Bacillus subtilis [TaxId:1423] [50285] (4 PDB entries)

   3. Species Escherichia coli [TaxId:562] [50284] (2 PDB entries)

   4. Species Thermotoga maritima [TaxId:243274] [69262] (1 PDB entry)

9. N-terminal domain of ribosomal protein L2 [50299] (2 species)
   incomplete OB-fold lacking the last strand

   1. Species Archaeon Haloarcula marismortui [TaxId:2238] [50301] (19 PDB entries)
      includes the N-terminal tail

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

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

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

    2. Species Thermotoga maritima [TaxId:243274] [110201] (1 PDB entry)

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

    • Species Escherichia coli [TaxId:562] [68911] (8 PDB entries)

12. Ribosomal protein S12 [50302] (1 species)

    • Species Thermus thermophilus [TaxId:274] [50303] (18 PDB entries)

13. Ribosomal protein S17 [50304] (2 species)

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

    2. Species Thermus thermophilus [TaxId:274] [50305] (18 PDB entries)

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

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

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

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

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

    2. Species Thermotoga maritima [TaxId:243274] [69266] (2 PDB entries)

16. 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)

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

    • Species Escherichia coli [TaxId:562] [110199] (3 PDB entries)

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

    • Species Human (Homo sapiens) [TaxId:9606] [117201] (1 PDB entry)

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

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

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

    • Species Escherichia coli [TaxId:562] [50291] (2 PDB entries)

21. 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)

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

    • Species Human (Homo sapiens) [TaxId:9606] [69264] (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 SCOP 1.69
  
• Family b.40.4.5: Cold shock DNA-binding domain-like appears in SCOP 1.73
  
• Family b.40.4.5: Cold shock DNA-binding domain-like appears in the current release, SCOPe 2.08