› 4eyi

X-ray diffraction
2.9Å resolution

Human DNA polymerase iota incorporating dATP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion

Released:
DOI: 10.2210/pdb4eyi/pdb
PDB entry 4eyi coloured by chain, front view.
PDB entry 4eyi coloured by chain, side view.
PDB entry 4eyi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase.
Kirouac KN, Basu AK, Ling H
Nucleic Acids Res 41 2060-71 (2013)
PMID: 23268450

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-117439 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase iota Chain: B
Molecule details ›
Chain: B
Length: 420 amino acids
Theoretical weight: 47.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UNA4 (Residues: 26-445; Coverage: 57%)
Gene names: POLI, RAD30B
Sequence domains:
Structure domains:
DNA template Chain: T
Molecule details ›
Chain: T
Length: 8 nucleotides
Theoretical weight: 2.67 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA primer Chain: P
Molecule details ›
Chain: P
Length: 7 nucleotides
Theoretical weight: 2.11 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 1 x DTP
Ligand MG 3 x MG
1 modified residue:
Ligand DG8 1 x DG8

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P6522
Unit cell:
a: 98.85Å b: 98.85Å c: 194.203Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.222 0.218 0.264
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Error-Prone and Error-Free Translesion DNA Synthesis over Site-Specifically Created DNA Adducts of Aryl Hydrocarbons (3-Nitrobenzanthrone and 4-Aminobiphenyl).
Yagi et al. (2017)
1 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