› 3h40

X-ray diffraction
2.3Å resolution

Binary complex of human DNA polymerase iota with template U/T

Released:
DOI: 10.2210/pdb3h40/pdb
PDB entry 3h40 coloured by chain, front view.
PDB entry 3h40 coloured by chain, side view.
PDB entry 3h40 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-116350 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase iota Chain: A
Molecule details ›
Chain: A
Length: 389 amino acids
Theoretical weight: 43.97 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q9UNA4 (Residues: 51-439; Coverage: 53%)
Gene names: POLI, RAD30B
Sequence domains:
Structure domains:
5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)-3' Chain: P
Molecule details ›
Chain: P
Length: 7 nucleotides
Theoretical weight: 2.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3' 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

1 bound ligand:
Ligand SO4 1 x SO4
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: 98.243Å b: 98.243Å c: 203.528Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.253 0.253 0.277
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

5 review citations

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

1 mention without citation

The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins.
Chakraborty et al. (2013)