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- PDB-9j5m: Cryo-EM structure of the ectodomain of BTN2A1-BTN3A1-BTN3A2 in co... -

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Basic information

Entry
Database: PDB / ID: 9j5m
TitleCryo-EM structure of the ectodomain of BTN2A1-BTN3A1-BTN3A2 in complex with gdTCR
Components
  • Butyrophilin subfamily 2 member A1
  • Butyrophilin subfamily 3 member A1
  • Butyrophilin subfamily 3 member A2
  • d subunit of gdTCR
  • g subunit of gdTCR
KeywordsIMMUNE SYSTEM / complex / immune
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / T cell mediated immunity / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / lipid metabolic process / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / signaling receptor binding ...Butyrophilin (BTN) family interactions / T cell mediated immunity / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / lipid metabolic process / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / signaling receptor binding / external side of plasma membrane / membrane / plasma membrane
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY domain / Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain ...Butyrophilin subfamily 1/2, SPRY/PRY domain / Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Butyrophilin subfamily 3 member A1 / Butyrophilin subfamily 3 member A2 / Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsZhu, Y. / Gao, W. / Huang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Immunity / Year: 2025
Title: Phosphoantigen-induced inside-out stabilization of butyrophilin receptor complexes drives dimerization-dependent γδ TCR activation.
Authors: Yuwei Zhu / Wenbo Gao / Jianlin Zheng / Ye Bai / Xinyu Tian / Tengjin Huang / Zebin Lu / De Dong / Anqi Zhang / Changyou Guo / Zhiwei Huang /
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 ...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.
History
DepositionAug 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: d subunit of gdTCR
B: g subunit of gdTCR
C: Butyrophilin subfamily 3 member A2
D: Butyrophilin subfamily 3 member A1
E: Butyrophilin subfamily 2 member A1
G: Butyrophilin subfamily 2 member A1
H: d subunit of gdTCR
I: g subunit of gdTCR


Theoretical massNumber of molelcules
Total (without water)299,2708
Polymers299,2708
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein d subunit of gdTCR


Mass: 22875.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein g subunit of gdTCR


Mass: 26056.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Butyrophilin subfamily 3 member A2 / BTN3A2


Mass: 33317.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A2, BT3.2, BTF3, BTF4 / Production host: Homo sapiens (human) / References: UniProt: P78410
#4: Protein Butyrophilin subfamily 3 member A1 / BTN3A1


Mass: 54432.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Production host: Homo sapiens (human) / References: UniProt: O00481
#5: Protein Butyrophilin subfamily 2 member A1 / BTN2A1


Mass: 56826.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN2A1, BT2.1, BTF1 / Production host: Homo sapiens (human) / References: UniProt: Q7KYR7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cryo-EM structure of BTN2A1-BTN3A1-BTN3A2 in complex with gdTCR
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 287533 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313257
ELECTRON MICROSCOPYf_angle_d0.73418039
ELECTRON MICROSCOPYf_dihedral_angle_d7.4041891
ELECTRON MICROSCOPYf_chiral_restr0.0472099
ELECTRON MICROSCOPYf_plane_restr0.0052316

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