› 3v6d

X-ray diffraction
2.7Å resolution

Crystal structure of HIV-1 reverse transcriptase (RT) cross-linked with AZT-terminated DNA

Released:
DOI: 10.2210/pdb3v6d/pdb
PDB entry 3v6d coloured by chain, front view.
PDB entry 3v6d coloured by chain, side view.
PDB entry 3v6d coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
Primary publication:
HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
Das K, Martinez SE, Bauman JD, Arnold E
Nat Struct Mol Biol 19 253-9 (2012)
PMID: 22266819

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.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117022 (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

No bound ligands
2 modified residues:
Ligand MRG 2 x MRG
Ligand ATM 2 x ATM

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P21
Unit cell:
a: 89.476Å b: 133.171Å c: 139.904Å
α: 90° β: 98.674° γ: 90°
R-values:
R R work R free
0.234 0.233 0.268
Expression system: Escherichia coli

Quick links

Citations

22 review citations

Molecular basis of human immunodeficiency virus type 1 drug resistance: overview and recent developments.
Menéndez-Arias L. (2013)
21 more

4 mentions without citation

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review.
Tarasova et al. (2018)
3 more