PDBe 4b3q

X-ray diffraction
5Å resolution

Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface

Released:

Function and Biology Details

Reactions catalysed:
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. 
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. 
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (4 distinct):
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 454 amino acids
Theoretical weight: 52.97 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli M15
UniProt:
  • Canonical: P04585 (Residues: 588-1027; Coverage: 31%)
Gene name: gag-pol
Sequence domains:
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 560 amino acids
Theoretical weight: 64.42 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli M15
UniProt:
  • Canonical: P04585 (Residues: 588-1147; Coverage: 39%)
Gene name: gag-pol
Sequence domains:
PRIMER DNA Chain: D
Molecule details ›
Chain: D
Length: 25 nucleotides
Theoretical weight: 7.67 KDa
TEMPLATE RNA Chain: R
Molecule details ›
Chain: R
Length: 34 nucleotides
Theoretical weight: 10.78 KDa

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: R32
Unit cell:
a: 272.7Å b: 272.7Å c: 233.1Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.363 0.361 0.407
Expression system: Escherichia coli M15