› 6m7v

X-ray diffraction
3.06Å resolution

Human DNA polymerase eta extension complex with cdA at the -1 position

Released:
DOI: 10.2210/pdb6m7v/pdb
PDB entry 6m7v coloured by chain, front view.
PDB entry 6m7v coloured by chain, side view.
PDB entry 6m7v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase η at atomic resolution.
Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W
Proc Natl Acad Sci U S A 115 10660-10665 (2018)
PMID: 30275308

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-120279 (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(P*GP*TP*GP*TP*GP*AP*GP*T)-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.5 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 9 nucleotides
Theoretical weight: 2.66 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand NI 1 x NI
Ligand DZ4 1 x DZ4
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 63.075Å b: 81.387Å c: 145.006Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.237 0.268
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

5',8-Cyclopurine Lesions in DNA Damage: Chemical, Analytical, Biological, and Diagnostic Significance.
Chatgilialoglu et al. (2019)
2 more

1 mention without citation

Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase η at atomic resolution.
Weng et al. (2018)