› 3os1

X-ray diffraction
2.97Å resolution

PFV target capture complex (TCC) at 2.97 A resolution

Released:
DOI: 10.2210/pdb3os1/pdb
PDB entry 3os1 coloured by chain, front view.
PDB entry 3os1 coloured by chain, side view.
PDB entry 3os1 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
OpenAccess logo 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-507785 (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*(2DA))-3') Chain: D
Molecule details ›
Chain: D
Length: 17 nucleotides
Theoretical weight: 5.18 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

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 2 x MG
Ligand SO4 1 x SO4
1 modified residue:
Ligand 2DA 1 x 2DA

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P41212
Unit cell:
a: 159.882Å b: 159.882Å c: 127.842Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.231 0.264
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

60 review citations

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

16 mentions without citation

Retroviral DNA Integration.
Lesbats et al. (2016)
15 more