› 5dgb

X-ray diffraction
1.79Å resolution

CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dA PAIR BY INSERTING dTMPNPP OPPOSITE TEMPLATE dA

Released:
DOI: 10.2210/pdb5dgb/pdb
PDB entry 5dgb coloured by chain, front view.
PDB entry 5dgb coloured by chain, side view.
PDB entry 5dgb coloured by chain, top view.
Source organisms:
Primary publication:
Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase η.
Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP, Egli M
J Biol Chem 291 14134-14145 (2016)
PMID: 27226627

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-509344 (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*AP*(EDA)P*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.67 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.44 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand GOL 2 x GOL
Ligand 1FZ 1 x 1FZ
1 modified residue:
Ligand EDA 1 x EDA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P61
Unit cell:
a: 98.66Å b: 98.66Å c: 82.004Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.166 0.164 0.212
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Formation and repair of oxidatively generated damage in cellular DNA.
Cadet et al. (2017)
1 more

1 mention without citation

Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase η.
Patra et al. (2016)