› 3gv5

X-ray diffraction
2Å resolution

Human DNA polymerase iota in complex with T template DNA and incoming ddADP

Released:
DOI: 10.2210/pdb3gv5/pdb
PDB entry 3gv5 coloured by chain, front view.
PDB entry 3gv5 coloured by chain, side view.
PDB entry 3gv5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota.
Kirouac KN, Ling H
EMBO J 28 1644-54 (2009)
PMID: 19440206

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-116341 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase iota Chains: B, D
Molecule details ›
Chains: B, D
Length: 420 amino acids
Theoretical weight: 47.59 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:
5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3' Chains: E, P
Molecule details ›
Chains: E, P
Length: 9 nucleotides
Theoretical weight: 2.84 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3' Chains: F, T
Molecule details ›
Chains: F, T
Length: 13 nucleotides
Theoretical weight: 3.85 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 8 x CA
Ligand GOL 1 x GOL
Ligand ADI 2 x ADI
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 140.16Å b: 71.75Å c: 127.42Å
α: 90° β: 112.53° γ: 90°
R-values:
R R work R free
0.206 0.205 0.253
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

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

8 mentions without citation

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