› 5dlg

X-ray diffraction
2.35Å resolution

Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine

Released:
DOI: 10.2210/pdb5dlg/pdb
PDB entry 5dlg coloured by chain, front view.
PDB entry 5dlg coloured by chain, side view.
PDB entry 5dlg coloured by chain, top view.
Source organisms:
Primary publication:
Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η.
O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ
Chem Sci 7 4896-4904 (2016)
PMID: 27574558

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-118574 (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(*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: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*TP*(5DB)P*AP*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P61
Unit cell:
a: 98.656Å b: 98.656Å c: 82.131Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.172 0.248
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 citation in other articles

Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis.
Xu et al. (2017)
4 more

2 mentions without citation

Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase η.
Patra et al. (2016)
1 more