PDBe 4u1j

X-ray diffraction
1.38Å resolution

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes

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. 
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Capsid protein p24 Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.03 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04585 (Residues: 180-188; Coverage: 1%)
Gene name: gag-pol
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
HLA class I histocompatibility antigen, B-42 alpha chain Chain: A
Molecule details ›
Chain: A
Length: 278 amino acids
Theoretical weight: 32.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P30480 (Residues: 25-301; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 50.91Å b: 81.74Å c: 111.22Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.196
Expression systems:
  • Not provided
  • Escherichia coli BL21(DE3)