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- PDB-8zjy: Cryo-EM structure of pAg-bound BTN2A1-BTN3A1-BTN3A3 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8zjy
TitleCryo-EM structure of pAg-bound BTN2A1-BTN3A1-BTN3A3 in complex with Vgamma9-Vdelta2 TCR (G115 genotype)
Components
  • (Butyrophilin subfamily 3 member ...) x 2
  • (T cell receptor ...) x 2
  • Butyrophilin subfamily 2 member A1
KeywordsIMMUNE SYSTEM / Receptor
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 / nuclear body ...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 / nuclear body / signaling receptor binding / external side of plasma membrane / intracellular membrane-bounded organelle / nucleoplasm / membrane / plasma membrane / cytosol
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
Chem-H6P / Butyrophilin subfamily 3 member A3 / Butyrophilin subfamily 3 member A1 / Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsXin, W. / Huang, B. / Su, Q. / Zhou, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100975 China
CitationJournal: Biorxiv / Year: 2025
Title: Phosphoantigen-Driven Dissociation of Butyrophilin Oligomers Activates gamma delta T Cells
Authors: Xin, W. / Huang, B. / Gao, W. / Zhang, W. / Hu, Y. / Liu, Y. / Liang, E. / Shi, Y. / Su, Q. / Zhou, Q.
History
DepositionMay 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyrophilin subfamily 2 member A1
B: Butyrophilin subfamily 2 member A1
D: T cell receptor delta variable 2, T cell receptor delta constant 1
E: Butyrophilin subfamily 3 member A3
F: Butyrophilin subfamily 3 member A1
G: T cell receptor gamma variable 9, T cell receptor gamma constant 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,4647
Polymers290,2026
Non-polymers2621
Water00
1


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

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Components

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T cell receptor ... , 2 types, 2 molecules DG

#2: Protein T cell receptor delta variable 2, T cell receptor delta constant 1


Mass: 22746.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: ExpiHEK293F / Cell line (production host): ExpiHEK293F / Production host: Homo sapiens (human)
#5: Protein T cell receptor gamma variable 9, T cell receptor gamma constant 1


Mass: 25927.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiHEK293F / Production host: Homo sapiens (human)

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Butyrophilin subfamily 3 member ... , 2 types, 2 molecules EF

#3: Protein Butyrophilin subfamily 3 member A3


Mass: 65729.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A3, BTF3 / Cell line (production host): ExpiHEK293F / Production host: Homo sapiens (human) / References: UniProt: O00478
#4: Protein Butyrophilin subfamily 3 member A1


Mass: 54428.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Cell line (production host): ExpiHEK293F / Production host: Homo sapiens (human) / References: UniProt: O00481

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Protein / Non-polymers , 2 types, 3 molecules AB

#1: Protein Butyrophilin subfamily 2 member A1


Mass: 60684.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN2A1, BT2.1, BTF1 / Cell line (production host): ExpiHEK293F / Production host: Homo sapiens (human) / References: UniProt: Q7KYR7
#6: Chemical ChemComp-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate


Mass: 262.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O8P2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Human BTN complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 213 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
4cryoSPARC4.4.1CTF correction
8PHENIXmodel refinement
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1023733
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 413213 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00519451
ELECTRON MICROSCOPYf_angle_d0.64726363
ELECTRON MICROSCOPYf_dihedral_angle_d5.3232627
ELECTRON MICROSCOPYf_chiral_restr0.0462882
ELECTRON MICROSCOPYf_plane_restr0.0063409

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