› 3dlr

X-ray diffraction
2.2Å resolution

Crystal structure of the catalytic core domain from PFV integrase

Released:
DOI: 10.2210/pdb3dlr/pdb
PDB entry 3dlr coloured by chain, front view.
PDB entry 3dlr coloured by chain, side view.
PDB entry 3dlr coloured by chain, top view.
Source organism: Human spumaretrovirus
Primary publication:
Functional and structural characterization of the integrase from the prototype foamy virus.
Valkov E, Gupta SS, Hare S, Helander A, Roversi P, McClure M, Cherepanov P
Nucleic Acids Res 37 243-55 (2009)
PMID: 19036793

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146935 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Integrase Chain: A
Molecule details ›
Chain: A
Length: 202 amino acids
Theoretical weight: 22.65 KDa
Source organism: Human spumaretrovirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P14350 (Residues: 859-1058; Coverage: 18%)
Gene name: pol
Sequence domains: Integrase core domain
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
1 modified residue:
Ligand MSE 1 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P6122
Unit cell:
a: 52.14Å b: 52.14Å c: 239.78Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.214 0.209 0.259
Expression system: Escherichia coli

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Citations

27 review citations

The structural biology of HIV-1: mechanistic and therapeutic insights.
Engelman et al. (2012)
26 more

7 mentions without citation

Structural biology of retroviral DNA integration.
Li et al. (2011)
6 more