› 3gim

X-ray diffraction
2.7Å resolution

Dpo4 extension ternary complex with oxoG(anti)-G(syn) pair

Released:
DOI: 10.2210/pdb3gim/pdb
PDB entry 3gim coloured by chain, front view.
PDB entry 3gim coloured by chain, side view.
PDB entry 3gim coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ
Structure 17 725-36 (2009)
PMID: 19446528

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116303 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 38.95 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 2-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DDG))-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 4.09 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3' Chain: E
Molecule details ›
Chain: E
Length: 18 nucleotides
Theoretical weight: 5.41 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DGT 1 x DGT
Ligand CA 3 x CA
2 modified residues:
Ligand DDG 1 x DDG
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21212
Unit cell:
a: 99.668Å b: 111.924Å c: 53.158Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.214 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine.
Beard et al. (2010)
1 more

4 mentions without citation

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