› 3kle

X-ray diffraction
3.2Å resolution

Crystal structure of AZT-resistant HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA

Released:
DOI: 10.2210/pdb3kle/pdb
PDB entry 3kle coloured by chain, front view.
PDB entry 3kle coloured by chain, side view.
PDB entry 3kle coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
Primary publication:
Structural basis of HIV-1 resistance to AZT by excision.
Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E
Nat Struct Mol Biol 17 1202-9 (2010)
PMID: 20852643

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-116487 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Reverse transcriptase/ribonuclease H Chains: A, E, I, M
Molecule details ›
Chains: A, E, I, M
Length: 562 amino acids
Theoretical weight: 64.76 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1159; Coverage: 39%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chains: B, F, J, N
Molecule details ›
Chains: B, F, J, N
Length: 437 amino acids
Theoretical weight: 51.12 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 (25-MER) Chains: C, G, K, O
Molecule details ›
Chains: C, G, K, O
Length: 27 nucleotides
Theoretical weight: 8.37 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*(2DA))-3') Chains: D, H, L, P
Molecule details ›
Chains: D, H, L, P
Length: 21 nucleotides
Theoretical weight: 6.46 KDa

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, Z9N
Carbohydrate polymer
3 bound ligands:
Ligand MG 8 x MG
Ligand ZP4 4 x ZP4
Ligand GOL 2 x GOL
2 modified residues:
Ligand MRG 4 x MRG
Ligand 2DA 4 x 2DA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 78.738Å b: 283.33Å c: 155.233Å
α: 90° β: 89.73° γ: 90°
R-values:
R R work R free
0.28 0.28 0.308
Expression system: Escherichia coli

Quick links

Citations

17 review citations

Approved Antiviral Drugs over the Past 50 Years.
De Clercq et al. (2016)
16 more

6 mentions without citation

The structural biology of HIV-1: mechanistic and therapeutic insights.
Engelman et al. (2012)
5 more