› 5kg0

X-ray diffraction
1.6Å resolution

Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mM Mn2+ for 1800s then with 5 mM Mn2+ for 60s at 22 degree

Released:
DOI: 10.2210/pdb5kg0/pdb
PDB entry 5kg0 coloured by chain, front view.
PDB entry 5kg0 coloured by chain, side view.
PDB entry 5kg0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis.
Gao Y, Yang W
Science 352 1334-7 (2016)
PMID: 27284197

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-118938 (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 BL21(DE3)
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*TP*A)-3') Chain: P
Molecule details ›
Chain: P
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MN 3 x MN
Ligand GOL 3 x GOL
Ligand DTP 1 x DTP
Ligand DPO 1 x DPO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P61
Unit cell:
a: 98.08Å b: 98.08Å c: 81.9Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.176 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

18 review citations

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism.
Yang et al. (2018)
17 more