› 6vmx

X-ray diffraction
3.1Å resolution

Structure of HD14 TCR in complex with HLA-B7 presenting an EBV epitope

Released:
DOI: 10.2210/pdb6vmx/pdb
PDB entry 6vmx coloured by chain, front view.
PDB entry 6vmx coloured by chain, side view.
PDB entry 6vmx coloured by chain, top view.
Source organisms:
Primary publication:
A Shared TCR Bias toward an Immunogenic EBV Epitope Dominates in HLA-B*07:02-Expressing Individuals.
Rowntree LC, Nguyen THO, Farenc C, Halim H, Hensen L, Rossjohn J, Kotsimbos TC, Purcell AW, Kedzierska K, Gras S, Mifsud NA
J Immunol 205 1524-1534 (2020)
PMID: 32817371

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-231690 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
HLA class I histocompatibility antigen, B alpha chain Chains: A, F
Molecule details ›
Chains: A, F
Length: 276 amino acids
Theoretical weight: 32.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P01889 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
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 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Epstein-Barr nuclear antigen 3 Chains: C, H
Molecule details ›
Chains: C, H
Length: 9 amino acids
Theoretical weight: 1.17 KDa
Source organism: Human herpesvirus 4 strain B95-8
Expression system: Not provided
UniProt:
  • Canonical: P12977 (Residues: 379-387; Coverage: 1%)
Gene names: BLRF3-BERF1, EBNA3
HD14 alpha chain Chains: D, I
Molecule details ›
Chains: D, I
Length: 203 amino acids
Theoretical weight: 22.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
HD14 beta chain Chains: E, J
Molecule details ›
Chains: E, J
Length: 243 amino acids
Theoretical weight: 27.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Ligands and Environments

2 bound ligands:
Ligand PEG 3 x PEG
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: C2221
Unit cell:
a: 165.459Å b: 181.089Å c: 190.292Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.221 0.242
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

6 citation in other articles

CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses.
Lineburg et al. (2021)
5 more

4 mentions without citation

TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers.
Szeto et al. (2020)
3 more