› 4wwk

X-ray diffraction
3.1Å resolution

Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin

Released:
DOI: 10.2210/pdb4wwk/pdb
PDB entry 4wwk coloured by chain, front view.
PDB entry 4wwk coloured by chain, side view.
PDB entry 4wwk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.
Le Nours J, Praveena T, Pellicci DG, Gherardin NA, Ross FJ, Lim RT, Besra GS, Keshipeddy S, Richardson SK, Howell AR, Gras S, Godfrey DI, Rossjohn J, Uldrich AP
Nat Commun 7 10570 (2016)
PMID: 26875526

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-100929 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
T cell receptor alpha chain constant; T cell receptor alpha variable 12-3 Chain: A
Molecule details ›
Chain: A
Length: 209 amino acids
Theoretical weight: 23.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0B4J271 (Residues: 22-114; Coverage: 100%)
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC, TRAV12-3
Sequence domains:
Structure domains: Immunoglobulins
T cell receptor beta constant 2; T cell receptor beta variable 6-5 Chain: B
Molecule details ›
Chain: B
Length: 243 amino acids
Theoretical weight: 27.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0K0K1A5 (Residues: 19-113; Coverage: 99%)
  • Canonical: A0A5B9 (Residues: 1-129; Coverage: 73%)
Gene names: TCRBC2, TRBC2, TRBV6-5
Sequence domains:
Structure domains: Immunoglobulins
Antigen-presenting glycoprotein CD1d Chain: C
Molecule details ›
Chain: C
Length: 278 amino acids
Theoretical weight: 31.5 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P15813 (Residues: 21-295; Coverage: 87%)
Gene name: CD1D
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: D
Molecule details ›
Chain: D
Length: 119 amino acids
Theoretical weight: 13.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61769 (Residues: 1-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand NAG 2 x NAG
Ligand JLS 1 x JLS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 56.38Å b: 76.07Å c: 255.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.195 0.256
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

7 review citations

Sphingolipid metabolism in cancer signalling and therapy.
Ogretmen B. (2018)
6 more

3 mentions without citation

Novel Molecular Insights into Human Lipid-Mediated T Cell Immunity.
Shahine et al. (2021)
2 more