› 3l2v

X-ray diffraction
3.2Å resolution

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese and MK0518 (Raltegravir)

Released:
DOI: 10.2210/pdb3l2v/pdb
PDB entry 3l2v coloured by chain, front view.
PDB entry 3l2v coloured by chain, side view.
PDB entry 3l2v coloured by chain, top view.
Source organism: Human spumaretrovirus
Primary publication:
Retroviral intasome assembly and inhibition of DNA strand transfer.
Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P
OpenAccess logo Nature 464 232-6 (2010)
PMID: 20118915

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:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116519 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 395 amino acids
Theoretical weight: 44.46 KDa
Source organism: Human spumaretrovirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P14350 (Residues: 752-1143; Coverage: 34%)
Gene name: pol
Sequence domains:
Structure domains:
5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.86 KDa
Source organism: Human spumaretrovirus
Expression system: Not provided
5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 17 nucleotides
Theoretical weight: 5.16 KDa
Source organism: Human spumaretrovirus
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand MN 3 x MN
Ligand NH4 1 x NH4
Ligand RLT 1 x RLT
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P41212
Unit cell:
a: 158.65Å b: 158.65Å c: 125.23Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.205 0.232
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

102 review citations

Approved Antiviral Drugs over the Past 50 Years.
De Clercq et al. (2016)
101 more

7 mentions without citation

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