SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

Lineage for Fold a.4: DNA/RNA-binding 3-helical bundle

  1. Root: SCOPe 2.06
  2. 1976409Class a: All alpha proteins [46456] (289 folds)
  3. 1981147Fold a.4: DNA/RNA-binding 3-helical bundle [46688] (14 superfamilies)
    core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down

Superfamilies:

  1. 1981148a.4.1: Homeodomain-like [46689] (20 families) (S)
    consists only of helices
  2. 1982136a.4.2: Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46767] (2 families) (S)
    automatically mapped to Pfam PF01035
  3. 1982162a.4.3: ARID-like [46774] (2 families) (S)
    contains extra helices at both N- and C-termini
  4. 1982196a.4.5: "Winged helix" DNA-binding domain [46785] (85 families) (S)
    contains a small beta-sheet (wing)
  5. 1984099a.4.6: C-terminal effector domain of the bipartite response regulators [46894] (4 families) (S)
    binds to DNA and RNA polymerase; the N-terminal, receiver domain belongs to the CheY family
  6. 1984251a.4.7: Ribosomal protein L11, C-terminal domain [46906] (1 family) (S)
  7. 1984365a.4.8: Ribosomal protein S18 [46911] (1 family) (S)
  8. 1984442a.4.9: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46915] (1 family) (S)
  9. 1984450a.4.10: N-terminal Zn binding domain of HIV integrase [46919] (1 family) (S)
  10. 1984474a.4.11: RNA polymerase subunit RPB10 [46924] (1 family) (S)
    automatically mapped to Pfam PF01194
  11. 1984523a.4.12: TrpR-like [48295] (4 families) (S)
    contains an extra shared helix after the HTH motif
  12. 1984585a.4.13: Sigma3 and sigma4 domains of RNA polymerase sigma factors [88659] (4 families) (S)
  13. 1984711a.4.14: KorB DNA-binding domain-like [109709] (1 family) (S)
    contains HTH motif in the common core; also contains extra N-terminal helix and C-terminal subdomain of 4 helices (left-handed superhelix)
  14. 1984729a.4.15: Rps17e-like [116820] (1 family) (S)
    automatically mapped to Pfam PF00833

More info for Fold a.4: DNA/RNA-binding 3-helical bundle

Timeline for Fold a.4: DNA/RNA-binding 3-helical bundle: