9O4X image
Deposition Date 2025-04-09
Release Date 2025-12-10
Last Version Date 2026-02-04
Entry Detail
PDB ID:
9O4X
Keywords:
Title:
Gamma delta T cell receptor bound to CD1d
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.86 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 43 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antigen-presenting glycoprotein CD1d
Gene (Uniprot):CD1D
Chain IDs:D (auth: A)
Chain Length:274
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Beta-2-microglobulin
Gene (Uniprot):B2M
Chain IDs:A (auth: B)
Chain Length:99
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:T cell receptor delta chain
Chain IDs:B (auth: D)
Chain Length:197
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:T cell receptor gamma chain
Chain IDs:C (auth: G)
Chain Length:224
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
gamma delta T cell receptor recognition of CD1d in a lipid-independent manner.
Nat Commun 17 926 926 (2025)
PMID: 41457154 DOI: 10.1038/s41467-025-67653-0

Abstact

The monomorphic antigen-presenting molecule CD1d presents lipid antigens to both αβ and γδ T cells. While type I natural killer T cells (NKT) display exquisite specificity for CD1d presenting α-galactosylceramide (α-GalCer), the extent of lipid specificity exhibited by CD1d-restricted γδ T cells remains unclear. Here, we demonstrate that human γδ T cell receptors (TCRs) can recognise CD1d in either a lipid-dependent or lipid-independent manner with weak to moderate affinity. Using small-angle X-Ray scattering, we find that γδ TCR-CD1d binding modality is conserved across distinct CD1d-restricted TCRs. In functional assays, CD1d γδ TCR affinity was a poor predictor of γδ T cell line activation. Moreover, CD1d presenting endogenous lipids was sufficient to stimulate T cell activation and induce γδ TCR-CD3 clustering and phosphorylation in a dose-dependent manner. Elongation of the γδ TCR-CD3 complex by the inclusion of the Cγ2 and Cγ3 -encoded constant domains perturbed cellular activation whilst maintaining the ability to form functional γδ TCR clusters. The crystal structure of a Vδ1 γδ+ TCR-CD1d complex showed that the γδ TCR sat atop of the CD1d antigen-binding cleft but made no contacts with the presented lipid antigen. These findings provide a molecular basis for lipid-independent CD1d recognition by γδ TCRs.

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Primary Citation of related structures
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