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- EMDB-39876: Cryo-EM structure of intracellular HBMBPP-BTN2A1-BTN3A1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39876
TitleCryo-EM structure of intracellular HBMBPP-BTN2A1-BTN3A1 complex
Map data
Sample
  • Complex: BTN2A1-BTN3A1
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 2 member A1
  • Ligand: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE
Keywordscomplex / immune / IMMUNE SYSTEM
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / 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 / 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 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZheng J / Gao W / Zhu Y / Huang Z
Funding support China, 1 items
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
DepositionApr 24, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39876.png

Downloads & links

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Map

FileDownload / File: emd_39876.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.4387317 - 5.2410517
Average (Standard dev.)0.00022216357 (±0.0499404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39876_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39876_half_map_2.map
Projections & Slices
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Sample components

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Entire : BTN2A1-BTN3A1

EntireName: BTN2A1-BTN3A1
Components
  • Complex: BTN2A1-BTN3A1
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 2 member A1
  • Ligand: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE

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Supramolecule #1: BTN2A1-BTN3A1

SupramoleculeName: BTN2A1-BTN3A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Butyrophilin subfamily 3 member A1

MacromoleculeName: Butyrophilin subfamily 3 member A1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.462047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EQELREMAWS TMKQEQSTRV KLLEELRWRS IQYASRGERH SAYNEWKKAL FKPADVILDP KTANPILLVS EDQRSVQRAK EPQDLPDNP ERFNWHYCVL GCESFISGRH YWEVEVGDRK EWHIGVCSKN VQRKGWVKMT PENGFWTMGL TDGNKYRTLT E PRTNLKLP ...String:
EQELREMAWS TMKQEQSTRV KLLEELRWRS IQYASRGERH SAYNEWKKAL FKPADVILDP KTANPILLVS EDQRSVQRAK EPQDLPDNP ERFNWHYCVL GCESFISGRH YWEVEVGDRK EWHIGVCSKN VQRKGWVKMT PENGFWTMGL TDGNKYRTLT E PRTNLKLP KTPKKVGVFL DYETGDISFY NAVDGSHIHT FLDVSFSEAL YPVFRILTLE PTALTICPA

UniProtKB: Butyrophilin subfamily 3 member A1

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Macromolecule #2: Butyrophilin subfamily 2 member A1

MacromoleculeName: Butyrophilin subfamily 2 member A1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.227328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WINKLQKEKK ILSGEKEFER ETREIALKEL EKERVQKEEE LQVKEKLQEE LRWRRTFLHA VDVVLDPDTA HPDLFLSEDR RSVRRCPFR HLGESVPDNP ERFDSQPCVL GRESFASGKH YWEVEVENVI EWTVGVCRDS VERKGEVLLI PQNGFWTLEM H KGQYRAVS ...String:
WINKLQKEKK ILSGEKEFER ETREIALKEL EKERVQKEEE LQVKEKLQEE LRWRRTFLHA VDVVLDPDTA HPDLFLSEDR RSVRRCPFR HLGESVPDNP ERFDSQPCVL GRESFASGKH YWEVEVENVI EWTVGVCRDS VERKGEVLLI PQNGFWTLEM H KGQYRAVS SPDRILPLKE SLCRVGVFLD YEAGDVSFYN MRDRSHIYTC PRSAFSVPVR PFFRLGCEDS PIFICPALTG AN GVTVPEE GLTLHRVGTH QSL

UniProtKB: Butyrophilin subfamily 2 member A1

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Macromolecule #3: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE

MacromoleculeName: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: EIP
Molecular weightTheoretical: 264.107 Da
Chemical component information

ChemComp-EIP:
4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 50 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 535747
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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