› 4o3p

X-ray diffraction
1.72Å resolution

Crystal structure of human polymerase eta inserting dctp opposite an 8-oxog containing dna template

Released:
DOI: 10.2210/pdb4o3p/pdb
PDB entry 4o3p coloured by chain, front view.
PDB entry 4o3p coloured by chain, side view.
PDB entry 4o3p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Kinetics, structure, and mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine bypass by human DNA polymerase η.
Patra A, Nagy LD, Zhang Q, Su Y, Müller L, Guengerich FP, Egli M
J Biol Chem 289 16867-82 (2014)
PMID: 24759104

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117896 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 48.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
Structure domains:
DNA (5'-D(*CP*AP*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand 0KX 1 x 0KX
Ligand MG 2 x MG
Ligand GOL 2 x GOL
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P61
Unit cell:
a: 98.198Å b: 98.198Å c: 81.551Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.165 0.163 0.208
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Excessive Reactive Oxygen Species and Exotic DNA Lesions as an Exploitable Liability.
AbdulSalam et al. (2016)
5 more

7 mentions without citation

Kinetics, structure, and mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine bypass by human DNA polymerase η.
Patra et al. (2014)
6 more