9O4X | pdb_00009o4x

Gamma delta T cell receptor bound to CD1d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 
    0.255 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

gamma delta T cell receptor recognition of CD1d in a lipid-independent manner.

Rice, M.T.Gunasinghe, S.D.Sok, C.L.Pan, M.Lay, C.S.Gully, B.S.Rossjohn, J.

(2025) Nat Commun 17: 926-926

  • DOI: https://doi.org/10.1038/s41467-025-67653-0
  • Primary Citation of Related Structures:  
    9O4X

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinA [auth B]99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor delta chainB [auth D]197Homo sapiensMutation(s): 0 
Entity Groups  
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Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor gamma chainC [auth G]224Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1dD [auth A]274Homo sapiensMutation(s): 0 
Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens)
Explore P15813 
Go to UniProtKB:  P15813
PHAROS:  P15813
GTEx:  ENSG00000158473 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15813
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P15813-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
F [auth E]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free:  0.255 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.093α = 90
b = 178.093β = 90
c = 75.428γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references
  • Version 1.2: 2026-01-21
    Changes: Database references
  • Version 1.3: 2026-02-04
    Changes: Database references