› 4ww2

X-ray diffraction
2.48Å resolution

Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin

Released:
DOI: 10.2210/pdb4ww2/pdb
PDB entry 4ww2 coloured by chain, front view.
PDB entry 4ww2 coloured by chain, side view.
PDB entry 4ww2 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-100946 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
T cell receptor alpha chain constant; T cell receptor alpha variable 21 Chain: A
Molecule details ›
Chain: A
Length: 207 amino acids
Theoretical weight: 22.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0B4J279 (Residues: 20-110; Coverage: 98%)
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC, TRAV21
Sequence domains:
Structure domains: Immunoglobulins
T cell receptor beta constant 2 Chain: B
Molecule details ›
Chain: B
Length: 243 amino acids
Theoretical weight: 27.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A5B9 (Residues: 1-129; Coverage: 73%)
Gene names: TCRBC2, TRBC2
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Antigen-presenting glycoprotein CD1d Chain: C
Molecule details ›
Chain: C
Length: 284 amino acids
Theoretical weight: 32.32 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: F
Molecule details ›
Chain: F
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61769 (Residues: 21-119; 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: C2
Unit cell:
a: 209.99Å b: 46.3Å c: 124.65Å
α: 90° β: 122.28° γ: 90°
R-values:
R R work R free
0.198 0.196 0.244
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