› 4bac

X-ray diffraction
3.26Å resolution

prototype foamy virus strand transfer complexes on product DNA

Released:
DOI: 10.2210/pdb4bac/pdb
PDB entry 4bac coloured by chain, front view.
PDB entry 4bac coloured by chain, side view.
PDB entry 4bac coloured by chain, top view.
Source organisms:
Primary publication:
Assembly of prototype foamy virus strand transfer complexes on product DNA bypassing catalysis of integration.
Yin Z, Lapkouski M, Yang W, Craigie R
Protein Sci 21 1849-57 (2012)
PMID: 23011895

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-117249 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 396 amino acids
Theoretical weight: 44.66 KDa
Source organism: Human spumaretrovirus
Expression system: Escherichia coli BL21(DE3)
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*AP)-3' Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.86 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (38-MER) Chain: D
Molecule details ›
Chain: D
Length: 38 nucleotides
Theoretical weight: 11.57 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3' Chain: E
Molecule details ›
Chain: E
Length: 17 nucleotides
Theoretical weight: 5.27 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P41212
Unit cell:
a: 160.617Å b: 160.617Å c: 125.092Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

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

3 mentions without citation

Assembly of prototype foamy virus strand transfer complexes on product DNA bypassing catalysis of integration.
Yin et al. (2012)
2 more