› 6nca

X-ray diffraction
3.3Å resolution

HLA-A2 (A*02:01) bound to a peptide from the Epstein-Barr virus BRLF1 protein

Released:
DOI: 10.2210/pdb6nca/pdb
PDB entry 6nca coloured by chain, front view.
PDB entry 6nca coloured by chain, side view.
PDB entry 6nca coloured by chain, top view.
Source organisms:
Primary publication:
CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection.
Kamga L, Gil A, Song I, Brody R, Ghersi D, Aslan N, Stern LJ, Selin LK, Luzuriaga K
PLoS Pathog 15 e1008122 (2019)
PMID: 31765434

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-137812 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Replication and transcription activator Chains: 1, 2, 3, 4, 5, 6, 7, 8, U, V, W, X, Y, Z, u, v, w, x, y, z
Molecule details ›
Chains: 1, 2, 3, 4, 5, 6, 7, 8, U, V, W, X, Y, Z, u, v, w, x, y, z
Length: 9 amino acids
Theoretical weight: 1.07 KDa
Source organism: human gammaherpesvirus 4
Expression system: Not provided
UniProt:
  • Canonical: Q3KSS7 (Residues: 109-117; Coverage: 2%)
Gene name: BRLF1
HLA class I histocompatibility antigen, A alpha chain Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Length: 275 amino acids
Theoretical weight: 31.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P04439 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-A, HLAA
Sequence domains:
Beta-2-microglobulin Chains: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t
Molecule details ›
Chains: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t
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

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 189.91Å b: 100.17Å c: 292.41Å
α: 90° β: 94.43° γ: 90°
R-values:
R R work R free
0.285 0.285 0.303
Expression systems:
  • Not provided
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

2 review citations

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors.
Lee et al. (2020)
1 more

1 mention without citation

The Use of Molecular Dynamics Simulation Method to Quantitatively Evaluate the Affinity between HBV Antigen T Cell Epitope Peptides and HLA-A Molecules.
Mei et al. (2022)