8ZA6 | pdb_00008za6

Cryo-EM structure of the gdTCR-CD3 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 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

Phosphoantigen-induced inside-out stabilization of butyrophilin receptor complexes drives dimerization-dependent gamma delta TCR activation.

Zhu, Y.Gao, W.Zheng, J.Bai, Y.Tian, X.Huang, T.Lu, Z.Dong, D.Zhang, A.Guo, C.Huang, Z.

(2025) Immunity 58: 1646-1659.e5

  • DOI: https://doi.org/10.1016/j.immuni.2025.04.012
  • Primary Citation of Related Structures:  
    8ZA6, 8ZA9, 8ZAA, 8ZAB, 8ZD4, 8ZYR, 9II6, 9IIK, 9J5J, 9J5M

  • PubMed Abstract: 

    Phosphoantigens (pAgs), produced by infected or cancer cells, trigger the assembly of a membrane receptor complex comprising butyrophilin (BTN) members BTN3A1 and BTN2A1, leading to the activation of γδ T cells. BTN3A2 or BTN3A3 forms heteromers with BTN3A1, exhibiting higher γδ T cell receptor (TCR)-stimulating activity than BTN3A1 homomers. Cryoelectron microscopy (cryo-EM) structure reveals a pAg-induced BTN2A1-BTN3A1 heterotetramer with a 2:2 stoichiometry, stabilized by interactions between the intracellular B30.2 domains and the extracellular immunoglobulin V (IgV) domains. BTN3A2 or BTN3A3 heterodimerizes with BTN3A1, forming a pAg-induced tetrameric complex with BTN2A1. However, BTN3A1 heterodimers are more stable than BTN3A1 homodimers in this interaction. Cryo-EM reveals that BTN2A1-BTN3A1-BTN3A2 binds two γδ TCR ectodomains, with one being sandwiched between the IgV domains of BTN2A1 and BTN3A2, while the other interacts with the free BTN2A1 IgV in the complex, as evidenced by functional data. Together, our findings uncover the mechanism of ligand-induced inside-out stabilization of BTN receptor complexes for dimeric activation of γδ TCR.


  • Organizational Affiliation
    • HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainA [auth a],
B [auth b]
165Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
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PHAROS:  P20963
GTEx:  ENSG00000198821 
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UniProt GroupP20963
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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
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PHAROS:  P04234
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
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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
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GTEx:  ENSG00000160654 
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UniProt GroupP09693
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TRA@ proteinG [auth m]290Homo sapiensMutation(s): 0 
Gene Names: TRA@
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CD3H [auth n]328Homo sapiensMutation(s): 0 
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:

Structure Validation

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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: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references