› 7sig

X-ray diffraction
1.74Å resolution

Crystal Structure of HLA B*3501 in complex with NPDIVIYQY, an 9-mer epitope from HIV-I

Released:
DOI: 10.2210/pdb7sig/pdb
PDB entry 7sig coloured by chain, front view.
PDB entry 7sig coloured by chain, side view.
PDB entry 7sig coloured by chain, top view.
Source organisms:
Entry authors: Gras S, Lobos CA, Chatzileontiadou DSM

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-221186 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q546I9 (Residues: 25-300; Coverage: 82%)
Gene name: HLA-B
Sequence domains:
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
p51 RT Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.12 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P03366 (Residues: 774-782; Coverage: 1%)
Gene name: gag-pol

Ligands and Environments

1 bound ligand:
Ligand FLC 1 x FLC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: R3
Unit cell:
a: 157.822Å b: 157.822Å c: 42.394Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.216
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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