› 4b3o

X-ray diffraction
3.3Å resolution

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

Released:
DOI: 10.2210/pdb4b3o/pdb
PDB entry 4b3o coloured by chain, front view.
PDB entry 4b3o coloured by chain, side view.
PDB entry 4b3o coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.
Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang W
Nat Struct Mol Biol 20 230-236 (2013)
PMID: 23314251

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-117232 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (4 distinct):
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:
Structure domains:
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 441 amino acids
Theoretical weight: 51.38 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:
Structure domains:
5'-D(*CP*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP*TP *TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 24 nucleotides
Theoretical weight: 7.37 KDa
5'-R(*AP*UP*GP*AP*3DRP*GP*GP*CP*CP*AP*CP*AP*AP*UP*AP *AP*CP*UP*AP*UP*AP*GP*GP*CP*AP*UP*A)-3' Chain: R
Molecule details ›
Chain: R
Length: 27 nucleotides
Theoretical weight: 8.54 KDa

Ligands and Environments

2 bound ligands:
Ligand EFZ 1 x EFZ
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3121
Unit cell:
a: 164.598Å b: 164.598Å c: 129.03Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.276 0.275 0.295
Expression system: Escherichia coli M15

Quick links

Citations

12 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
11 more

12 mentions without citation

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