PDBe 5hp1

X-ray diffraction
2.9Å resolution

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A DNA aptamer and FOSCARNET, a Pyrophosphate analog

Released:

Function and Biology Details

Reactions catalysed:
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.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Reverse transcriptase/ribonuclease H Chains: A, C
Molecule details ›
Chains: A, C
Length: 555 amino acids
Theoretical weight: 63.88 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1154; Coverage: 38%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chains: B, D
Molecule details ›
Chains: B, D
Length: 444 amino acids
Theoretical weight: 51.93 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1027; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:
DNA (38-MER) Chains: E, F
Molecule details ›
Chains: E, F
Length: 38 nucleotides
Theoretical weight: 11.75 KDa

Ligands and Environments


1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P21
Unit cell:
a: 90.325Å b: 129.069Å c: 131.542Å
α: 90° β: 101° γ: 90°
R-values:
R R work R free
0.247 0.246 0.273
Expression system: Escherichia coli