PDBe 3v4i

X-ray diffraction
2.8Å resolution

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and AZTTP

Released:

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.
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 Chains: A, C
Molecule details ›
Chains: A, C
Length: 556 amino acids
Theoretical weight: 64.02 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1153; Coverage: 38%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chains: B, D
Molecule details ›
Chains: B, D
Length: 428 amino acids
Theoretical weight: 50.04 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 (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') Chains: E, T
Molecule details ›
Chains: E, T
Length: 27 nucleotides
Theoretical weight: 8.42 KDa
DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3') Chains: F, P
Molecule details ›
Chains: F, P
Length: 21 nucleotides
Theoretical weight: 6.49 KDa

Ligands and Environments

2 bound ligands:

2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P21
Unit cell:
a: 90.053Å b: 132.647Å c: 138.014Å
α: 90° β: 98.12° γ: 90°
R-values:
R R work R free
0.23 0.229 0.262
Expression system: Escherichia coli