X-ray diffraction
2.53Å resolution

HIV-1 reverse transcriptase in complex with DNA that has incorporated EFdA-MP at the P-(post-translocation) site and a second EFdA-MP at the N-(pre-translocation) site


Function and Biology Details

Reactions catalysed:
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
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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 560 amino acids
Theoretical weight: 64.52 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
  • Canonical: P04585 (Residues: 588-1147; Coverage: 39%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 440 amino acids
Theoretical weight: 51.38 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli
  • Canonical: P04585 (Residues: 588-1027; Coverage: 31%)
Gene name: gag-pol
Sequence domains:
Structure domains:
Molecule details ›
Chain: P
Length: 22 nucleotides
Theoretical weight: 6.87 KDa
DNA (27-MER) Chain: T
Molecule details ›
Chain: T
Length: 27 nucleotides
Theoretical weight: 8.4 KDa

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: C2221
Unit cell:
a: 165.977Å b: 170.183Å c: 99.695Å
α: 90° β: 90° γ: 90°
R R work R free
0.196 0.193 0.246
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli