› 4j9m

X-ray diffraction
2.25Å resolution

Human DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after an A at the primer 3' end (AA/G)

Released:
DOI: 10.2210/pdb4j9m/pdb
PDB entry 4j9m coloured by chain, front view.
PDB entry 4j9m coloured by chain, side view.
PDB entry 4j9m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η.
Zhao Y, Gregory MT, Biertümpfel C, Hua YJ, Hanaoka F, Yang W
Proc Natl Acad Sci U S A 110 8146-51 (2013)
PMID: 23630267

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-117688 (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 Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA Chain: P
Molecule details ›
Chain: P
Length: 9 nucleotides
Theoretical weight: 2.71 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand NA 1 x NA
Ligand XG4 1 x XG4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P61
Unit cell:
a: 98.43Å b: 98.43Å c: 82.01Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.18 0.223
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Translesion DNA polymerases in eukaryotes: what makes them tick?
Vaisman et al. (2017)
5 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