› 8gon

X-ray diffraction
2.6Å resolution

SARS-CoV-2 specific private TCR RLQ7 in complex with RLQ-T1006I-HLA-A2

Released:
DOI: 10.2210/pdb8gon/pdb
PDB entry 8gon coloured by chain, front view.
PDB entry 8gon coloured by chain, side view.
PDB entry 8gon coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor (TCR) diversity.
Wu D, Efimov GA, Bogolyubova AV, Pierce BG, Mariuzza RA
J Biol Chem 103035 (2023)
PMID: 36806685

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-227497 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A140T913 (Residues: 25-299; Coverage: 79%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
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 S2' Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.12 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Synthecium
UniProt:
  • Canonical: P0DTC2 (Residues: 1000-1008; Coverage: 1%)
Gene names: 2, S
SARS-CoV-2 specific private TCR RLQ7 alpha Chain: D
Molecule details ›
Chain: D
Length: 207 amino acids
Theoretical weight: 23.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
SARS-CoV-2 specific private TCR RLQ7 beta Chain: E
Molecule details ›
Chain: E
Length: 246 amino acids
Theoretical weight: 27.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P6522
Unit cell:
a: 147.366Å b: 147.366Å c: 178.819Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.198 0.253
Expression systems:
  • Escherichia coli
  • Synthecium

Quick links

Citations

2 citation in other articles

Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features.
Shcherbinin et al. (2023)
1 more

1 mention without citation

Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor diversity.
Wu et al. (2023)