› 3h4d

X-ray diffraction
2.2Å resolution

Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP

Released:
DOI: 10.2210/pdb3h4d/pdb
PDB entry 3h4d coloured by chain, front view.
PDB entry 3h4d coloured by chain, side view.
PDB entry 3h4d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Replication across template T/U by human DNA polymerase-iota.
Jain R, Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK
Structure 17 974-80 (2009)
PMID: 19604477

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-116352 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase iota Chain: A
Molecule details ›
Chain: A
Length: 390 amino acids
Theoretical weight: 44.04 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q9UNA4 (Residues: 50-439; Coverage: 53%)
Gene names: POLI, RAD30B
Sequence domains:
Structure domains:
5'-D(*AP*GP*GP*AP*CP*CP*(DOC)) Chain: P
Molecule details ›
Chain: P
Length: 7 nucleotides
Theoretical weight: 2.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T) Chain: T
Molecule details ›
Chain: T
Length: 9 nucleotides
Theoretical weight: 2.8 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand DGT 1 x DGT
2 modified residues:
Ligand DOC 1 x DOC
Ligand BRU 1 x BRU

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P6522
Unit cell:
a: 97.915Å b: 97.915Å c: 203.392Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.254 0.254 0.27
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

3 review citations

Separate roles of structured and unstructured regions of Y-family DNA polymerases.
Ohmori et al. (2009)
2 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