› 3ohb

X-ray diffraction
2Å resolution

Yeast DNA polymerase eta extending from an 8-oxoG lesion

Released:
DOI: 10.2210/pdb3ohb/pdb
PDB entry 3ohb coloured by chain, front view.
PDB entry 3ohb coloured by chain, side view.
PDB entry 3ohb coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase η.
Silverstein TD, Jain R, Johnson RE, Prakash L, Prakash S, Aggarwal AK
Structure 18 1463-70 (2010)
PMID: 21070945

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-116652 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 520 amino acids
Theoretical weight: 58.81 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q04049 (Residues: 1-513; Coverage: 81%)
Gene names: DBH1, RAD30, YDR419W
Sequence domains: impB/mucB/samB family
Structure domains:
5'-D(*TP*AP*AP*TP*GP*(8OG)P*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 5.07 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3' Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.21 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DCP 1 x DCP
Ligand MG 2 x MG
Ligand SO4 3 x SO4
2 modified residues:
Ligand 8OG 1 x 8OG
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 87.958Å b: 228.268Å c: 85.932Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.156 0.188
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Eukaryotic translesion synthesis: Choosing the right tool for the job.
Powers et al. (2018)
4 more

3 mentions without citation

DNA polymerases provide a canon of strategies for translesion synthesis past oxidatively generated lesions.
Zahn et al. (2011)
2 more