› 1c6v

X-ray diffraction
3Å resolution

SIV INTEGRASE (CATALYTIC DOMAIN + DNA BIDING DOMAIN COMPRISING RESIDUES 50-293) MUTANT WITH PHE 185 REPLACED BY HIS (F185H)

Released:
DOI: 10.2210/pdb1c6v/pdb
PDB entry 1c6v coloured by chain, front view.
PDB entry 1c6v coloured by chain, side view.
PDB entry 1c6v coloured by chain, top view.
Source organism: Simian immunodeficiency virus
Primary publication:
X-ray structure of simian immunodeficiency virus integrase containing the core and C-terminal domain (residues 50-293)--an initial glance of the viral DNA binding platform.
Chen Z, Yan Y, Munshi S, Li Y, Zugay-Murphy J, Xu B, Witmer M, Felock P, Wolfe A, Sardana V, Emini EA, Hazuda D, Kuo LC
J Mol Biol 296 521-33 (2000)
PMID: 10669606

Function and Biology Details

Reactions catalysed: 
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183401 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
PROTEIN (SIV INTEGRASE) Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 164 amino acids
Theoretical weight: 18.41 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q88016 (Residues: 817-980; Coverage: 16%)
Gene name: pol
Sequence domains: Integrase core domain
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
PROTEIN (SIU89134) Chain: X
Molecule details ›
Chain: X
Length: 81 amino acids
Theoretical weight: 9.19 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q88016 (Residues: 980-1060; Coverage: 8%)
Gene name: pol
Sequence domains: Integrase DNA binding domain
Structure domains: Integrase, C-terminal domain superfamily, retroviral

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 79.57Å b: 100Å c: 150.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.203 0.362
Expression system: Escherichia coli K-12

Quick links

Citations

7 review citations

Retroviral integrase inhibitors year 2000: update and perspectives.
Pommier et al. (2000)
6 more

10 mentions without citation

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