PDBe 3kk3

X-ray diffraction
2.9Å resolution

HIV-1 reverse transcriptase-DNA complex with GS-9148 terminated primer

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
2 distinct DNA molecules
Macromolecules (4 distinct):
p51 RT Chain: B
Molecule details ›
Chain: B
Length: 452 amino acids
Theoretical weight: 52.75 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 588-1027; Coverage: 31%)
Gene name: gag-pol
Sequence domains:
Structure domains:
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 560 amino acids
Theoretical weight: 64.52 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 588-1147; Coverage: 39%)
Gene name: gag-pol
Sequence domains:
Structure domains:
5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*C*(URT))-3' Chain: P
Molecule details ›
Chain: P
Length: 21 nucleotides
Theoretical weight: 6.4 KDa
5'-D(*AP*TP*GP*GP*TP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3' Chain: T
Molecule details ›
Chain: T
Length: 27 nucleotides
Theoretical weight: 8.4 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2221
Unit cell:
a: 166.998Å b: 169.07Å c: 96.398Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.223 0.287
Expression system: Escherichia coli BL21(DE3)