› 3os2

X-ray diffraction
3.32Å resolution

PFV target capture complex (TCC) at 3.32 A resolution

Released:
DOI: 10.2210/pdb3os2/pdb
PDB entry 3os2 coloured by chain, front view.
PDB entry 3os2 coloured by chain, side view.
PDB entry 3os2 coloured by chain, top view.
Source organism: Human spumaretrovirus
Primary publication:
The mechanism of retroviral integration from X-ray structures of its key intermediates.
Maertens GN, Hare S, Cherepanov P
Nature 468 326-9 (2010)
PMID: 21068843

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 decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116669 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 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:
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.83 KDa
Source organism: Human spumaretrovirus
Expression system: Not provided
DNA (5'-D(*TP*GP*CP*GP*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: 5.2 KDa
Source organism: Human spumaretrovirus
Expression system: Not provided
DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 30 nucleotides
Theoretical weight: 9.23 KDa
Source organism: Human spumaretrovirus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P41212
Unit cell:
a: 160.951Å b: 160.951Å c: 127.933Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.224 0.26
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

62 review citations

HIV DNA integration.
Craigie et al. (2012)
61 more

8 mentions without citation

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