8ZYR | pdb_00008zyr

Cryo-EM structure of BTN2A1-BTN3A1-BTN3A3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 2 member A1
A, D
499Homo sapiensMutation(s): 0 
Gene Names: BTN2A1BT2.1BTF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KYR7 (Homo sapiens)
Explore Q7KYR7 
Go to UniProtKB:  Q7KYR7
PHAROS:  Q7KYR7
GTEx:  ENSG00000112763 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7KYR7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A1484Homo sapiensMutation(s): 1 
Gene Names: BTN3A1BTF5
UniProt & NIH Common Fund Data Resources
Find proteins for O00481 (Homo sapiens)
Explore O00481 
Go to UniProtKB:  O00481
PHAROS:  O00481
GTEx:  ENSG00000026950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00481
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A3555Homo sapiensMutation(s): 0 
Gene Names: BTN3A3BTF3
UniProt & NIH Common Fund Data Resources
Find proteins for O00478 (Homo sapiens)
Explore O00478 
Go to UniProtKB:  O00478
PHAROS:  O00478
GTEx:  ENSG00000111801 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00478
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H6P (Subject of Investigation/LOI)
Query on H6P

Download Ideal Coordinates CCD File 
E [auth B](2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
C5 H12 O8 P2
MDSIZRKJVDMQOQ-GORDUTHDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:

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: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references