› 4rnn

X-ray diffraction
1.81Å resolution

Crystal structure of human polymerase eta inserting dGMPnPP opposite DNA template containing an abasic site

Released:
DOI: 10.2210/pdb4rnn/pdb
PDB entry 4rnn coloured by chain, front view.
PDB entry 4rnn coloured by chain, side view.
PDB entry 4rnn coloured by chain, top view.
Source organisms:
Primary publication:
Structural and kinetic analysis of nucleoside triphosphate incorporation opposite an abasic site by human translesion DNA polymerase η.
Patra A, Zhang Q, Lei L, Su Y, Egli M, Guengerich FP
J Biol Chem 290 8028-38 (2015)
PMID: 25666608

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-118109 (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:
Nucleic acids Template: CAT(3DR)ATGACGCT Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.51 KDa
Source organism: synthetic construct
Expression system: Not provided
Nucleic acids Primar: AGCGTCAT Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P61
Unit cell:
a: 98.556Å b: 98.556Å c: 81.88Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.168 0.203
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance.
McNeill et al. (2020)
3 more

2 mentions without citation

Structural and kinetic analysis of nucleoside triphosphate incorporation opposite an abasic site by human translesion DNA polymerase η.
Patra et al. (2015)
1 more