› 7wj2

X-ray diffraction
1.28Å resolution

Crystal structure of HLA-C*1402 complexed with 8-mer HIV gag peptide

Released:
DOI: 10.2210/pdb7wj2/pdb
PDB entry 7wj2 coloured by chain, front view.
PDB entry 7wj2 coloured by chain, side view.
PDB entry 7wj2 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding.
Asa M, Morita D, Kuroha J, Mizutani T, Mori N, Mikami B, Sugita M
J Biol Chem 298 102100 (2022)
PMID: 35667438

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-105969 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 277 amino acids
Theoretical weight: 32.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A858LG55 (Residues: 24-300; Coverage: 81%)
Gene name: HLA-C
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 20-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Matrix protein p17 Chain: C
Molecule details ›
Chain: C
Length: 8 amino acids
Theoretical weight: 894 Da
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04591 (Residues: 78-85; Coverage: 2%)
Gene name: gag

Ligands and Environments

3 bound ligands:
Ligand EDO 7 x EDO
Ligand NA 1 x NA
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: C2
Unit cell:
a: 92.655Å b: 76.885Å c: 62.053Å
α: 90° β: 119.54° γ: 90°
R-values:
R R work R free
0.157 0.156 0.178
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 mention without citation

Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding.
Asa et al. (2022)