› 3m9m

X-ray diffraction
2.9Å resolution

Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion

Released:
DOI: 10.2210/pdb3m9m/pdb
PDB entry 3m9m coloured by chain, front view.
PDB entry 3m9m coloured by chain, side view.
PDB entry 3m9m coloured by chain, top view.
Source organisms:
Primary publication:
Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4.
Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling H
EMBO J 29 2059-69 (2010)
PMID: 20512114

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-116552 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: B
Molecule details ›
Chain: B
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*G)-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.15 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.35 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21212
Unit cell:
a: 98.576Å b: 101.193Å c: 52.418Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.286 0.285 0.309
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea.
Peng et al. (2017)
3 more

3 mentions without citation

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