› 8gvb

X-ray diffraction
3.2Å resolution

The complex between public TCR TD08 and HLA-A24 bound to HIV-1 Nef138-8 peptide

Released:
DOI: 10.2210/pdb8gvb/pdb
PDB entry 8gvb coloured by chain, front view.
PDB entry 8gvb coloured by chain, side view.
PDB entry 8gvb coloured by chain, top view.
Source organisms:
Primary publication:
Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors.
Ma K, Chai Y, Guan J, Tan S, Qi J, Kawana-Tachikawa A, Dong T, Iwamoto A, Shi Y, Gao GF
J Immunol (2022)
PMID: 36130828

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-224816 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
TD08 TCR alpha chain Chain: A
Molecule details ›
Chain: A
Length: 209 amino acids
Theoretical weight: 23.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
TD08 TCR beta chain Chain: B
Molecule details ›
Chain: B
Length: 246 amino acids
Theoretical weight: 28.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Ig-like domain-containing protein Chain: H
Molecule details ›
Chain: H
Length: 275 amino acids
Theoretical weight: 31.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: F6IQZ4 (Residues: 25-298; Coverage: 88%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chain: L
Molecule details ›
Chain: L
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
C-terminal core protein Chain: P
Molecule details ›
Chain: P
Length: 8 amino acids
Theoretical weight: 1.04 KDa
Source organism: HIV-1 06TG.HT008
Expression system: Not provided
UniProt:
  • Canonical: P04601 (Residues: 134-141; Coverage: 4%)
Gene name: nef

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P3221
Unit cell:
a: 71.657Å b: 71.657Å c: 381.651Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.282 0.28 0.321
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 citation in other articles

Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.
Bekker et al. (2023)
1 more