› 4q8f

X-ray diffraction
2.8Å resolution

Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G

Released:
DOI: 10.2210/pdb4q8f/pdb
PDB entry 4q8f coloured by chain, front view.
PDB entry 4q8f coloured by chain, side view.
PDB entry 4q8f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and mechanistic studies of polymerase η bypass of phenanthriplatin DNA damage.
Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W, Lippard SJ
Proc Natl Acad Sci U S A 111 9133-8 (2014)
PMID: 24927576

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-118010 (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 BL21(DE3)
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
Structure domains:
5'-D(*CP*AP*TP*CP*GP*TP*CP*AP*CP*AP*CP*T)-3' Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*AP*GP*TP*GP*TP*GP*AP*C)-3' Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.47 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P61
Unit cell:
a: 98.692Å b: 98.692Å c: 81.812Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.196 0.243
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

The Next Generation of Platinum Drugs: Targeted Pt(II) Agents, Nanoparticle Delivery, and Pt(IV) Prodrugs.
Johnstone et al. (2016)
5 more

1 mention without citation

Structural and mechanistic studies of polymerase η bypass of phenanthriplatin DNA damage.
Gregory et al. (2014)