› 1rtd

X-ray diffraction
3.2Å resolution

STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE

Released:
DOI: 10.2210/pdb1rtd/pdb
PDB entry 1rtd coloured by chain, front view.
PDB entry 1rtd coloured by chain, side view.
PDB entry 1rtd coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.
Huang H, Chopra R, Verdine GL, Harrison SC
Science 282 1669-75 (1998)
PMID: 9831551

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114541 (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: 554 amino acids
Theoretical weight: 63.87 KDa
Source organism: Human immunodeficiency virus 1
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: 440 amino acids
Theoretical weight: 51.4 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P04585 (Residues: 588-1027; Coverage: 31%)
Gene name: gag-pol
Sequence domains:
Structure domains:
DNA TEMPLATE FOR REVERSE TRANSCRIPTASE Chains: E, G
Molecule details ›
Chains: E, G
Length: 27 nucleotides
Theoretical weight: 8.33 KDa
DNA PRIMER FOR REVERSE TRANSCRIPTASE Chains: F, H
Molecule details ›
Chains: F, H
Length: 21 nucleotides
Theoretical weight: 6.42 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand TTP 2 x TTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 78.84Å b: 150.7Å c: 280.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.224 0.298
Expression system: Escherichia coli

Quick links

Citations

125 review citations

DNA replication fidelity.
Kunkel et al. (2000)
124 more

153 mentions without citation

HIV-1 antiretroviral drug therapy.
Arts et al. (2012)
152 more