8JBV | pdb_00008jbv

Extracellular domain of gamma delta TCR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8JBV

This is version 1.3 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 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), which is 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 , revealing 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 and connecting peptides. The length of the connecting peptides regulates the ligand association and T cell activation. A cholesterol-like molecule wedges into the transmembrane region, exerting an inhibitory role in TCR signalling. The Vγ5Vδ1 TCR-CD3 complex displays a dimeric architecture, whereby two protomers nestle back to back through the Vγ5 domains of the TCR extracellular domains. 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 unique properties of γδ TCR 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, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 144.15 kDa 
  • Atom Count: 6,624 
  • Modeled Residue Count: 824 
  • Deposited Residue Count: 1,276 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor delta variable 1,T cell receptor delta constantA [auth m],
C [auth M]
307Homo sapiensMutation(s): 0 
Gene Names: TRDV1TRDC
UniProt & NIH Common Fund Data Resources
Find proteins for A0A1B0GX56 (Homo sapiens)
Explore A0A1B0GX56 
Go to UniProtKB:  A0A1B0GX56
GTEx:  ENSG00000211804 
Find proteins for B7Z8K6 (Homo sapiens)
Explore B7Z8K6 
Go to UniProtKB:  B7Z8K6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsB7Z8K6A0A1B0GX56
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor gamma variable 5,T cell receptor gamma constant 1B [auth n],
D [auth N]
331Homo sapiensMutation(s): 0 
Gene Names: TRGV5TCRGV5TRGC1TCRGC1
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J1U4 (Homo sapiens)
Explore A0A0B4J1U4 
Go to UniProtKB:  A0A0B4J1U4
GTEx:  ENSG00000211697 
Find proteins for P0CF51 (Homo sapiens)
Explore P0CF51 
Go to UniProtKB:  P0CF51
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0CF51A0A0B4J1U4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)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
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-23
    Changes: Data collection