› 2dpi

X-ray diffraction
2.3Å resolution

Ternary complex of hPoli with DNA and dCTP

Released:
DOI: 10.2210/pdb2dpi/pdb
PDB entry 2dpi coloured by chain, front view.
PDB entry 2dpi coloured by chain, side view.
PDB entry 2dpi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota.
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK
Nat Struct Mol Biol 13 619-25 (2006)
PMID: 16819516

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 domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115180 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase iota Chain: A
Molecule details ›
Chain: A
Length: 420 amino acids
Theoretical weight: 47.03 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q9UNA4 (Residues: 26-445; Coverage: 57%)
Gene names: POLI, RAD30B
Sequence domains:
Structure domains:
5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-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(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3' Chain: T
Molecule details ›
Chain: T
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand DCP 1 x DCP
2 modified residues:
Ligand DOC 1 x DOC
Ligand EDA 1 x EDA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P6522
Unit cell:
a: 98.148Å b: 98.148Å c: 203.112Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.228 0.278
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

15 review citations

Translesion DNA polymerases in eukaryotes: what makes them tick?
Vaisman et al. (2017)
14 more

12 mentions without citation

Structural diversity of the Y-family DNA polymerases.
Pata JD. (2010)
11 more