3SCM image
Deposition Date 2011-06-08
Release Date 2011-10-05
Last Version Date 2024-10-16
Entry Detail
PDB ID:
3SCM
Keywords:
Title:
Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-isoglobotrihexosylceramide
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.31
R-Value Work:
0.27
R-Value Observed:
0.27
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Antigen-presenting glycoprotein CD1d1
Gene (Uniprot):Cd1d1
Chain IDs:A
Chain Length:302
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Beta-2-microglobulin
Gene (Uniprot):B2m
Chain IDs:B
Chain Length:99
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:NKT TCR Valpha14 chain
Chain IDs:C
Chain Length:207
Number of Molecules:1
Biological Source:Mus musculus , Homo sapiens
Polymer Type:polypeptide(L)
Molecule:NKT TCR autoreactive-Vbeta6 chain
Chain IDs:D
Chain Length:245
Number of Molecules:1
Biological Source:Mus musculus , Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Primary Citation
Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors
Nat.Immunol. 12 827 833 (2011)
PMID: 21804559 DOI: 10.1038/ni.2076

Abstact

The most potent foreign antigens for natural killer T cells (NKT cells) are α-linked glycolipids, whereas NKT cell self-reactivity involves weaker recognition of structurally distinct β-linked glycolipid antigens. Here we provide the mechanism for the autoreactivity of T cell antigen receptors (TCRs) on NKT cells to the mono- and tri-glycosylated β-linked agonists β-galactosylceramide (β-GalCer) and isoglobotrihexosylceramide (iGb3), respectively. In binding these disparate antigens, the NKT cell TCRs docked onto CD1d similarly, achieving this by flattening the conformation of the β-linked ligands regardless of the size of the glycosyl head group. Unexpectedly, the antigenicity of iGb3 was attributable to its terminal sugar group making compensatory interactions with CD1d. Thus, the NKT cell TCR molds the β-linked self ligands to resemble the conformation of foreign α-linked ligands, which shows that induced-fit molecular mimicry can underpin the self-reactivity of NKT cell TCRs to β-linked antigens.

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Primary Citation of related structures