› 5i3u

X-ray diffraction
3Å resolution

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE N-SITE COMPLEX; CATALYTIC INCORPORATION OF AZTMP to A DNA aptamer in CRYSTAL

Released:
DOI: 10.2210/pdb5i3u/pdb
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PDB entry 5i3u coloured by chain, front view.
PDB entry 5i3u coloured by chain, side view.
PDB entry 5i3u coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
Primary publication:
Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet.
Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E
ACS Chem Biol 11 2158-64 (2016)
PMID: 27192549

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118773 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (4 distinct):
Reverse transcriptase/ribonuclease H Chains: A, C
Molecule details ›
Chains: A, C
Length: 555 amino acids
Theoretical weight: 63.88 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1154; Coverage: 38%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chains: B, D
Molecule details ›
Chains: B, D
Length: 444 amino acids
Theoretical weight: 51.93 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1027; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:
DNA (39-MER) Chains: E, F

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
2 bound ligands:
Ligand MG 2 x MG
Ligand GOL 2 x GOL
2 modified residues:
Ligand OMC 4 x OMC
Ligand ATM 2 x ATM

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 90.24Å b: 128.71Å c: 131.66Å
α: 90° β: 100.84° γ: 90°
R-values:
R R work R free
0.224 0.223 0.254
Expression system: Escherichia coli

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Citations

4 review citations

Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance.
Xavier Ruiz et al. (2020)
3 more

2 mentions without citation

Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet.
Das et al. (2016)
1 more

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