› 7f4w

X-ray diffraction
2.9Å resolution

Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4

Released:
DOI: 10.2210/pdb7f4w/pdb
PDB entry 7f4w coloured by chain, front view.
PDB entry 7f4w coloured by chain, side view.
PDB entry 7f4w coloured by chain, top view.
Source organisms:
Primary publication:
Profiling CD8+ T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.
Zhang H, Deng S, Ren L, Zheng P, Hu X, Jin T, Tan X
Cell Rep 36 109708 (2021)
PMID: 34506741

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-113034 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 308 amino acids
Theoretical weight: 35.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: D9UAY1 (Residues: 25-300; Coverage: 88%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 102 amino acids
Theoretical weight: 12.09 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 S1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 9 amino acids
Theoretical weight: 1.27 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 448-456; 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: NFPSS BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 47.44Å b: 135.6Å c: 153.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.244 0.298
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

The Robustness of Cellular Immunity Determines the Fate of SARS-CoV-2 Infection.
Moga et al. (2022)
8 more

4 mentions without citation

Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity.
Mengist et al. (2021)
3 more