› 2rdj

X-ray diffraction
2.2Å resolution

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

Released:
DOI: 10.2210/pdb2rdj/pdb
PDB entry 2rdj coloured by chain, front view.
PDB entry 2rdj coloured by chain, side view.
PDB entry 2rdj coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4.
Wong JH, Fiala KA, Suo Z, Ling H
J Mol Biol 379 317-30 (2008)
PMID: 18448122

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218921 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 14 nucleotides
Theoretical weight: 4.28 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(P*DTP*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3') Chain: D
Molecule details ›
Chain: D
Length: 16 nucleotides
Theoretical weight: 4.89 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(P*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3') Chain: F
Molecule details ›
Chain: F
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 4 x CA
Ligand TMP 1 x TMP
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 97.993Å b: 102.51Å c: 106.109Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.21 0.256
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Separate roles of structured and unstructured regions of Y-family DNA polymerases.
Ohmori et al. (2009)
5 more

16 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
15 more