PDBe 3w39

X-ray diffraction
3.1Å resolution

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
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, B-52 alpha chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 277 amino acids
Theoretical weight: 32.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P30490 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, E
Molecule details ›
Chains: B, E
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
p51 RT Chains: C, F
Molecule details ›
Chains: C, F
Length: 8 amino acids
Theoretical weight: 849 Da
Source organism: Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Expression system: Not provided
UniProt:
  • Canonical: P12499 (Residues: 716-723; Coverage: 1%)
Gene name: gag-pol

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 69.045Å b: 83.255Å c: 170.347Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.298 0.295 0.347
Expression systems:
  • Escherichia coli
  • Not provided