› 3mfh

X-ray diffraction
2Å resolution

DNA Polymerase Eta in Complex With Undamaged DNA

Released:
DOI: 10.2210/pdb3mfh/pdb
PDB entry 3mfh coloured by chain, front view.
PDB entry 3mfh coloured by chain, side view.
PDB entry 3mfh coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis for the suppression of skin cancers by DNA polymerase eta.
Silverstein TD, Johnson RE, Jain R, Prakash L, Prakash S, Aggarwal AK
Nature 465 1039-43 (2010)
PMID: 20577207

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-116560 (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(*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
5'-D(*TP*AP*AP*TP*TP*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 5.03 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DTP 1 x DTP
Ligand SO4 2 x SO4
Ligand MG 2 x MG
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: C2221
Unit cell:
a: 88.745Å b: 227.935Å c: 85.967Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.194 0.227
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

17 review citations

Y-family DNA polymerases and their role in tolerance of cellular DNA damage.
Sale et al. (2012)
16 more

4 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
3 more