5yrs

X-ray diffraction
1.76Å resolution

X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrahedral Intermediate and Its SIHB with Catalytic Aspartate

Released:

Function and Biology Details

Reactions catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
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.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Protease Chain: A
Molecule details ›
Chain: A
Length: 104 amino acids
Theoretical weight: 11.16 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 489-587; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Protease Chain: B
Molecule details ›
Chain: B
Length: 104 amino acids
Theoretical weight: 11.1 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 489-587; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
p15 Chain: X
Molecule details ›
Chain: X
Length: 6 amino acids
Theoretical weight: 775 Da
Source organism: HIV-1 M:B_HXB2R
Expression system: Not provided
UniProt:
  • Canonical: P04585 (Residues: 1025-1030; Coverage: 0%)
Gene name: gag-pol

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P61
Unit cell:
a: 62.56Å b: 62.56Å c: 81.86Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.223 0.223 0.25
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided