› 7pbe

X-ray diffraction
3Å resolution

Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope

Released:
DOI: 10.2210/pdb7pbe/pdb
PDB entry 7pbe coloured by chain, front view.
PDB entry 7pbe coloured by chain, side view.
PDB entry 7pbe coloured by chain, top view.
Source organisms:
Primary publication:
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope.
Dolton G, Rius C, Hasan MS, Wall A, Szomolay B, Behiry E, Whalley T, Southgate J, Fuller A, Morin T, Topley K, Tan LR, Goulder PJR, Spiller OB, Rizkallah PJ, Jones LC, Connor TR, Sewell AK
Cell 185 2936-2951.e19 (2022)
PMID: 35931021

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-224576 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Ig-like domain-containing protein Chains: A, F
Molecule details ›
Chains: A, F
Length: 276 amino acids
Theoretical weight: 31.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A140T913 (Residues: 25-300; Coverage: 80%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chains: B, G
Molecule details ›
Chains: B, G
Length: 100 amino acids
Theoretical weight: 11.88 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: C, H
Molecule details ›
Chains: C, H
Length: 9 amino acids
Theoretical weight: 1.15 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTC2 (Residues: 269-277; Coverage: 1%)
Gene names: 2, S
Human T-cell Receptor YLQ36, alpha chain Chains: D, I
Molecule details ›
Chains: D, I
Length: 203 amino acids
Theoretical weight: 22.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Human T-cell Receptor YLQ36, beta chain Chains: E, J
Molecule details ›
Chains: E, J
Length: 243 amino acids
Theoretical weight: 27.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand PEG 2 x PEG
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 229.24Å b: 46.45Å c: 184.72Å
α: 90° β: 96.75° γ: 90°
R-values:
R R work R free
0.231 0.228 0.296
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

The biological and clinical significance of emerging SARS-CoV-2 variants.
Tao et al. (2021)
12 more

3 mentions without citation

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