8JC0

V gamma9 V delta2 TCR and CD3 complex in LMNG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens)
Explore P20963 
Go to UniProtKB:  P20963
PHAROS:  P20963
GTEx:  ENSG00000198821 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20963
Sequence Annotations
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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
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens)
Go to UniProtKB:  P04234
PHAROS:  P04234
GTEx:  ENSG00000167286 
Sequence Annotations
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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
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens)
Go to UniProtKB:  P07766
PHAROS:  P07766
GTEx:  ENSG00000198851 
Sequence Annotations
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  • Reference Sequence
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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
UniProt & NIH Common Fund Data Resources
Find proteins for P09693 (Homo sapiens)
Go to UniProtKB:  P09693
PHAROS:  P09693
GTEx:  ENSG00000160654 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor delta variable 2,T cell receptor delta constantG [auth m]310Homo sapiensMutation(s): 0 
Gene Names: TRDV2hDV102S1TRDC
UniProt & NIH Common Fund Data Resources
Find proteins for A0JD36 (Homo sapiens)
Go to UniProtKB:  A0JD36
GTEx:  ENSG00000211821 
Find proteins for B7Z8K6 (Homo sapiens)
Go to UniProtKB:  B7Z8K6
PHAROS:  B7Z8K6
Sequence Annotations
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor gamma variable 9,T cell receptor gamma constant 1H [auth n]332Homo sapiensMutation(s): 0 
Gene Names: TRGV9TCRGV9TRGC1TCRGC1
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Find proteins for P0CF51 (Homo sapiens)
Go to UniProtKB:  P0CF51
Find proteins for Q99603 (Homo sapiens)
Go to UniProtKB:  Q99603
GTEx:  ENSG00000211695 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32022037
National Natural Science Foundation of China (NSFC)China82241081

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