› 5ejk

X-ray diffraction
3.8Å resolution

Crystal structure of the Rous sarcoma virus intasome

Released:
DOI: 10.2210/pdb5ejk/pdb
PDB entry 5ejk coloured by chain, front view.
PDB entry 5ejk coloured by chain, side view.
PDB entry 5ejk coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of the Rous sarcoma virus intasome.
Yin Z, Shi K, Banerjee S, Pandey KK, Bera S, Grandgenett DP, Aihara H
Nature 530 362-6 (2016)
PMID: 26887497

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 hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118637 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Integrase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 270 amino acids
Theoretical weight: 30.57 KDa
Source organism: Rous sarcoma virus - Prague C
Expression system: Escherichia coli
UniProt:
  • Canonical: P03354 (Residues: 1281-1550; Coverage: 17%)
Gene name: gag-pol
Sequence domains:
RSV Integrase Chains: I, L
Molecule details ›
Chains: I, L
Length: 42 nucleotides
Theoretical weight: 13.05 KDa
Source organism: Rous sarcoma virus (strain Schmidt-Ruppin E)
Expression system: Escherichia coli
DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*TP*AP*CP*TP*C)-3') Chains: J, M
Molecule details ›
Chains: J, M
Length: 22 nucleotides
Theoretical weight: 6.72 KDa
Source organism: Rous sarcoma virus (strain Schmidt-Ruppin E)
Expression system: Not provided
DNA (5'-D(*CP*TP*TP*CP*TP*CP*TP*C)-3') Chains: K, N
Molecule details ›
Chains: K, N
Length: 8 nucleotides
Theoretical weight: 2.34 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*GP*TP*GP*TP*CP*TP*T)-3') Chains: k, n
Molecule details ›
Chains: k, n
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand W 36 x W
1 modified residue:
Ligand MSE 88 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 124.936Å b: 157.854Å c: 126.583Å
α: 90° β: 110.94° γ: 90°
R-values:
R R work R free
0.256 0.254 0.294
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

17 review citations

Integration site selection by retroviruses and transposable elements in eukaryotes.
Sultana et al. (2017)
16 more

15 mentions without citation

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