8WYI

T cell receptor delta 2 gamma 9 with TCRD TM domain chimera of TRAC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of human gamma delta T cell receptor-CD3 complex.

Xin, W.Huang, B.Chi, X.Liu, Y.Xu, M.Zhang, Y.Li, X.Su, Q.Zhou, Q.

(2024) Nature 630: 222-229

  • DOI: https://doi.org/10.1038/s41586-024-07439-4
  • Primary Citation of Related Structures:  
    8JBV, 8JC0, 8JCB, 8WXE, 8WY0, 8WYI, 8YC0

  • PubMed Abstract: 

    Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology 1-3 . The γδ T cell receptor (TCR), generated by γδ T cells, recognizes a diverse range of antigens independently of the major histocompatibility complex 2 . The γδ TCR associates with CD3 subunits, initiating T cell activation and holding great potential in immunotherapy 4 . Here, we report the structures of two prototypical human Vγ9Vδ2 and Vγ5Vδ1 TCR-CD3 complexes 5,6 , unveiling two distinct assembly mechanisms that depend on Vγ usage. The Vγ9Vδ2 TCR-CD3 complex is monomeric, with considerable conformational flexibility in the TCRγ/TCRδ extracellular domain (ECD) and connecting peptides (CPs). The length of CPs regulates the ligand association and T cell activation. Additionally, a cholesterol-like molecule wedges into the transmembrane region, exerting an inhibitory role in TCR signaling. The Vγ5Vδ1 TCR-CD3 complex displays a dimeric architecture, where two protomers nestle back-to-back via their Vγ5 domains of TCR ECDs. Our biochemical and biophysical assays further corroborate the dimeric structure. Importantly, the dimeric form of the Vγ5Vδ1 TCR is essential for T cell activation. These findings reveal organizing principles of the γδ TCR-CD3 complex, providing insights into the γδ TCR unique properties and facilitating immunotherapeutic interventions.


  • Organizational Affiliation

    Research Center for Industries of the Future, Center for Infectious Disease Research, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainA [auth a],
B [auth b]
195Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Membrane Entity: Yes 
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Find proteins for P20963 (Homo sapiens)
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GTEx:  ENSG00000198821 
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UniProt GroupP20963
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainC [auth d]171Homo sapiensMutation(s): 0 
Gene Names: CD3DT3D
Membrane Entity: Yes 
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Find proteins for P04234 (Homo sapiens)
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GTEx:  ENSG00000167286 
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UniProt GroupP04234
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainD [auth e],
E [auth f]
207Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
Membrane Entity: Yes 
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Find proteins for P07766 (Homo sapiens)
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GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainF [auth g]182Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
Membrane Entity: Yes 
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GTEx:  ENSG00000160654 
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UniProt GroupP09693
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Signal peptide,flag tag,T cell receptor delta variable 2,T cell receptor delta constant,T cell receptor alpha chain constant,T cell receptor delta variable 2,T cell receptor delta constant,T cell receptor alpha chain constantG [auth m]310Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000211821 
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UniProt GroupsA0JD36P01848B7Z8K6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Signal peptide,flag tag,T cell receptor gamma variable 9,T cell receptor gamma constant 1,T cell receptor gamma variable 9,T cell receptor gamma constant 1H [auth n]332Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q99603 (Homo sapiens)
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GTEx:  ENSG00000211695 
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UniProt GroupsQ99603P0CF51
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references