› 3huj

X-ray diffraction
2.5Å resolution

Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor

Released:
DOI: 10.2210/pdb3huj/pdb
PDB entry 3huj coloured by chain, front view.
PDB entry 3huj coloured by chain, side view.
PDB entry 3huj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors.
Pellicci DG, Patel O, Kjer-Nielsen L, Pang SS, Sullivan LC, Kyparissoudis K, Brooks AG, Reid HH, Gras S, Lucet IS, Koh R, Smyth MJ, Mallevaey T, Matsuda JL, Gapin L, McCluskey J, Godfrey DI, Rossjohn J
Immunity 31 47-59 (2009)
PMID: 19592275

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-233988 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Antigen-presenting glycoprotein CD1d Chains: A, C
Molecule details ›
Chains: A, 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 Chains: B, D
Molecule details ›
Chains: B, D
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
NKT15 T cell receptor alpha-chain Chains: E, G
Molecule details ›
Chains: E, G
Length: 209 amino acids
Theoretical weight: 23.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
NKT15 T cell receptor beta-chain Chains: F, H
Molecule details ›
Chains: F, H
Length: 246 amino acids
Theoretical weight: 28.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, NDG
Carbohydrate polymer
3 bound ligands:
Ligand NAG 2 x NAG
Ligand AGH 2 x AGH
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P2
Unit cell:
a: 112.112Å b: 82.36Å c: 117.184Å
α: 90° β: 101.26° γ: 90°
R-values:
R R work R free
0.219 0.216 0.279
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

44 review citations

Raising the NKT cell family.
Godfrey et al. (2010)
43 more

17 mentions without citation

Recognition of CD1d-restricted antigens by natural killer T cells.
Rossjohn et al. (2012)
16 more