› 5txl

X-ray diffraction
2.5Å resolution

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING DATP

Released:
DOI: 10.2210/pdb5txl/pdb
PDB entry 5txl coloured by chain, front view.
PDB entry 5txl coloured by chain, side view.
PDB entry 5txl coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
Primary publication:
Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance.
Das K, Martinez SE, Arnold E
Antimicrob Agents Chemother 61 (2017)
PMID: 28396546

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-509808 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Reverse transcriptase/ribonuclease H Chains: A, C
Molecule details ›
Chains: A, C
Length: 556 amino acids
Theoretical weight: 64.02 KDa
Source organism: Human immunodeficiency virus type 1 BH10
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: 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 (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3') Chains: E, T
Molecule details ›
Chains: E, T
Length: 27 nucleotides
Theoretical weight: 8.38 KDa
DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*GP)-3') Chains: F, P
Molecule details ›
Chains: F, P
Length: 21 nucleotides
Theoretical weight: 6.49 KDa

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
4 bound ligands:
Ligand MG 4 x MG
Ligand DTP 2 x DTP
Ligand SO4 1 x SO4
Ligand EDO 5 x EDO
1 modified residue:
Ligand MRG 2 x MRG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 90.38Å b: 133.846Å c: 139.34Å
α: 90° β: 97.3° γ: 90°
R-values:
R R work R free
0.194 0.193 0.224
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

8 mentions without citation

Avoiding Drug Resistance in HIV Reverse Transcriptase.
Cilento et al. (2021)
7 more