9J5J | pdb_00009j5j

Cryo-EM structure of BTN2A1-BTN3A1-BTN3A2 in complex with gdTCR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 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

  • DOI: https://doi.org/10.1016/j.immuni.2025.04.012
  • Primary Citation of Related Structures:  
    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
d domain of gdTCRA,
G [auth H]
205Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
g domain of gdTCRB,
H [auth I]
230Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0CF51 (Homo sapiens)
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Go to UniProtKB:  P0CF51
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UniProt GroupP0CF51
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A2305Homo sapiensMutation(s): 0 
Gene Names: BTN3A2BT3.2BTF3BTF4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P78410 (Homo sapiens)
Explore P78410 
Go to UniProtKB:  P78410
PHAROS:  P78410
GTEx:  ENSG00000186470 
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UniProt GroupP78410
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A1484Homo sapiensMutation(s): 1 
Gene Names: BTN3A1BTF5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O00481 (Homo sapiens)
Explore O00481 
Go to UniProtKB:  O00481
PHAROS:  O00481
GTEx:  ENSG00000026950 
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UniProt GroupO00481
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 2 member A1E,
F [auth G]
499Homo sapiensMutation(s): 0 
Gene Names: BTN2A1BT2.1BTF1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KYR7 (Homo sapiens)
Explore Q7KYR7 
Go to UniProtKB:  Q7KYR7
PHAROS:  Q7KYR7
GTEx:  ENSG00000112763 
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UniProt GroupQ7KYR7
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Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth J]4N/A
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth K]3N/A
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
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 
K [auth D](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: 4.05 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: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references