› 7wt3

X-ray diffraction
1.89Å resolution

Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide

Released:
DOI: 10.2210/pdb7wt3/pdb
PDB entry 7wt3 coloured by chain, front view.
PDB entry 7wt3 coloured by chain, side view.
PDB entry 7wt3 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-105410 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 277 amino acids
Theoretical weight: 31.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A5H2UYS3 (Residues: 26-302; Coverage: 81%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chains: B, E
Molecule details ›
Chains: B, E
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
4-mer lipopeptide Chains: C, F
Molecule details ›
Chains: C, F
Length: 5 amino acids
Theoretical weight: 618 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand TRS 1 x TRS
Ligand ACT 3 x ACT
Ligand ZN 3 x ZN
Ligand EDO 37 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P21
Unit cell:
a: 87.069Å b: 46.41Å c: 142.67Å
α: 90° β: 104.873° γ: 90°
R-values:
R R work R free
0.201 0.199 0.235
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)