› 4ed2

X-ray diffraction
1.71Å resolution

Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 7.2 (Na+ HEPES) with 1 Ca2+ ion

Released:
DOI: 10.2210/pdb4ed2/pdb
PDB entry 4ed2 coloured by chain, front view.
PDB entry 4ed2 coloured by chain, side view.
PDB entry 4ed2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Watching DNA polymerase η make a phosphodiester bond.
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W
OpenAccess logo Nature 487 196-201 (2012)
PMID: 22785315

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-508375 (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*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.64 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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P61
Unit cell:
a: 98.786Å b: 98.786Å c: 82.431Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.17 0.206
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

31 review citations

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

2 mentions without citation

Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
Opron et al. (2016)
1 more