› 8t4z

X-ray diffraction
2.69Å resolution

T-cell receptor and lipid complex structure

Released:
DOI: 10.2210/pdb8t4z/pdb
Model geometry
Fit model/data
PDB entry 8t4z coloured by chain, front view.
PDB entry 8t4z coloured by chain, side view.
PDB entry 8t4z coloured by chain, top view.
Source organisms:
Primary publication:
Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells.
Cheng TY, Praveena T, Govindarajan S, Almeida CF, Pellicci DG, Arkins WC, Van Rhijn I, Venken K, Elewaut D, Godfrey DI, Rossjohn J, Moody DB
Proc Natl Acad Sci U S A 121 e2321686121 (2024)
PMID: 39141352

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-268581 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Antigen-presenting glycoprotein CD1d1 Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Ig-like domain-containing protein Chain: C
Ig-like domain-containing protein; T cell receptor beta chain MC.7.G5 Chain: D

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand Y73 1 x Y73
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 57.906Å b: 79.036Å c: 242.373Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.193 0.265
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

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