› 1hys

X-ray diffraction
3Å resolution

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH A POLYPURINE TRACT RNA:DNA

Released:
DOI: 10.2210/pdb1hys/pdb
PDB entry 1hys coloured by chain, front view.
PDB entry 1hys coloured by chain, side view.
PDB entry 1hys coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
Sarafianos SG, Das K, Tantillo C, Clark AD, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E
EMBO J 20 1449-61 (2001)
PMID: 11250910

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-224749 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (6 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 553 amino acids
Theoretical weight: 63.75 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1152; Coverage: 38%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 425 amino acids
Theoretical weight: 49.56 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1024; Coverage: 29%)
Gene name: gag-pol
Sequence domains:
Structure domains:
FAB-28 MONOCLONAL ANTIBODY FRAGMENT LIGHT CHAIN Chain: C
Molecule details ›
Chain: C
Length: 214 amino acids
Theoretical weight: 22.93 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
FAB-28 MONOCLONAL ANTIBODY FRAGMENT HEAVY CHAIN Chain: D
Molecule details ›
Chain: D
Length: 220 amino acids
Theoretical weight: 23.46 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*GP*GP*CP*TP*G)-3' Chain: F
Molecule details ›
Chain: F
Length: 22 nucleotides
Theoretical weight: 6.75 KDa
5'-R(*UP*CP*AP*GP*CP*CP*AP*CP*UP*UP*UP*UP*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3' Chain: E
Molecule details ›
Chain: E
Length: 23 nucleotides
Theoretical weight: 7.34 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P3212
Unit cell:
a: 166.16Å b: 166.16Å c: 218.81Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.274 0.274 0.316
Expression system: Escherichia coli

Quick links

Citations

32 review citations

Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.
Sarafianos et al. (2009)
31 more

44 mentions without citation

RNase H activity: structure, specificity, and function in reverse transcription.
Schultz et al. (2008)
43 more