› 1r0a

X-ray diffraction
2.8Å resolution

Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms

Released:
DOI: 10.2210/pdb1r0a/pdb
PDB entry 1r0a coloured by chain, front view.
PDB entry 1r0a coloured by chain, side view.
PDB entry 1r0a coloured by chain, top view.
Source organisms:
Primary publication:
Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA.
Peletskaya EN, Kogon AA, Tuske S, Arnold E, Hughes SH
J Virol 78 3387-97 (2004)
PMID: 15016861

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 domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-207780 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 558 amino acids
Theoretical weight: 64.25 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1157; Coverage: 39%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 429 amino acids
Theoretical weight: 50.15 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1028; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:
monoclonal antibody (light chain) Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 23.36 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
Ig gamma-1 chain C region secreted form Chain: H
Molecule details ›
Chain: H
Length: 225 amino acids
Theoretical weight: 24 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P01868 (Residues: 1-102; Coverage: 32%)
Gene names: Igh-4, Ighg1
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
5'-D(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*GP*GP*T)-3' Chain: T
Molecule details ›
Chain: T
Length: 27 nucleotides
Theoretical weight: 8.37 KDa
5'-D(*C*CP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*AP*GP*CP*GP*CP*CP*GP*(2DA))-3' Chain: P
Molecule details ›
Chain: P
Length: 21 nucleotides
Theoretical weight: 6.36 KDa

Ligands and Environments

3 bound ligands:
Ligand GOL 2 x GOL
Ligand MG 1 x MG
Ligand GLC 1 x GLC
1 modified residue:
Ligand 2DA 1 x 2DA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P3212
Unit cell:
a: 165.82Å b: 165.82Å c: 220.72Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.239 0.239 0.272
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Past and future. Current drugs targeting HIV-1 integrase and reverse transcriptase-associated ribonuclease H activity: single and dual active site inhibitors.
Esposito et al. (2014)
4 more

7 mentions without citation

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