PDBe 6bj2

X-ray diffraction
3.35Å 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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
TCR 589 alpha chain Chain: D
Molecule details ›
Chain: D
Length: 206 amino acids
Theoretical weight: 23.28 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
TCR 589 beta chain Chain: E
Molecule details ›
Chain: E
Length: 241 amino acids
Theoretical weight: 27.19 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
HLA class I histocompatibility antigen, B-35 alpha chain Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.94 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P30685 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
p51 RT Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.01 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04585 (Residues: 880-888; Coverage: 1%)
Gene name: gag-pol

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 156.48Å b: 59.28Å c: 123.57Å
α: 90° β: 110.77° γ: 90°
R-values:
R R work R free
0.247 0.245 0.276
Expression systems:
  • Trichoplusia ni
  • Not provided