› 7ejl

X-ray diffraction
1.89Å resolution

Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein

Released:
DOI: 10.2210/pdb7ejl/pdb
PDB entry 7ejl coloured by chain, front view.
PDB entry 7ejl coloured by chain, side view.
PDB entry 7ejl coloured by chain, top view.
Source organisms:
Primary publication:
Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2.
Shimizu K, Iyoda T, Sanpei A, Nakazato H, Okada M, Ueda S, Kato-Murayama M, Murayama K, Shirouzu M, Harada N, Hidaka M, Fujii SI
Commun Biol 4 1365 (2021)
PMID: 34857854

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-105405 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 281 amino acids
Theoretical weight: 32.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A5H2UYS3 (Residues: 27-300; Coverage: 80%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 106 amino acids
Theoretical weight: 12.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Spike protein S2' Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.3 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 1208-1216; Coverage: 1%)
Gene names: 2, S

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P212121
Unit cell:
a: 67.717Å b: 85.465Å c: 91.373Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.255
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19.
Kockelbergh et al. (2022)
1 more

1 mention without citation

Seeing the T cell Immunity of SARS-CoV-2 and SARS-CoV: Believing the Epitope-Oriented Vaccines.
Yue et al. (2023)