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- EMDB-60591: Cryo-EM structure of the intracellular domains of BTN2A1-BTN3A1-BTN3A3 -

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Basic information

Entry
Database: EMDB / ID: EMD-60591
TitleCryo-EM structure of the intracellular domains of BTN2A1-BTN3A1-BTN3A3
Map data
Sample
  • Complex: complex
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A3
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
Keywordscomplex / immune / protein / IMMUNE SYSTEM
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
Butyrophilin subfamily 3 member A3 / Butyrophilin subfamily 3 member A1 / Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGao W / Zheng J / 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
DepositionJun 19, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60591.png

Downloads & links

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Map

FileDownload / File: emd_60591.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-0.8235384 - 1.9751414
Average (Standard dev.)-0.00022880989 (±0.030829303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60591_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60591_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : complex

EntireName: complex
Components
  • Complex: complex
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A3
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate

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Supramolecule #1: complex

SupramoleculeName: complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Butyrophilin subfamily 2 member A1

MacromoleculeName: Butyrophilin subfamily 2 member A1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.4434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KEKKILSGEK EFERETREIA LKELEKERVQ KEEELQVKEK LQEELRWRRT FLHAVDVVLD PDTAHPDLFL SEDRRSVRRC PFRHLGESV PDNPERFDSQ PCVLGRESFA SGKHYWEVEV ENVIEWTVGV CRDSVERKGE VLLIPQNGFW TLEMHKGQYR A VSSPDRIL ...String:
KEKKILSGEK EFERETREIA LKELEKERVQ KEEELQVKEK LQEELRWRRT FLHAVDVVLD PDTAHPDLFL SEDRRSVRRC PFRHLGESV PDNPERFDSQ PCVLGRESFA SGKHYWEVEV ENVIEWTVGV CRDSVERKGE VLLIPQNGFW TLEMHKGQYR A VSSPDRIL PLKESLCRVG VFLDYEAGDV SFYNMRDRSH IYTCPRSAFS VPVRPFFRLG CEDSPIFICP ALTGANGVTV PE EGLTLHR VGTHQSL

UniProtKB: Butyrophilin subfamily 2 member A1

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Macromolecule #2: Butyrophilin subfamily 3 member A1

MacromoleculeName: Butyrophilin subfamily 3 member A1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.056969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEKKTQFRKK KREQELREMA WSTMKQEQST RVKLLEELRW RSIQYASRGE RHSAYNEWKK ALFKPADVIL DPKTANPILL VSEDQRSVQ RAKEPQDLPD NPERFNWHYC VLGCESFISG RHYWEVEVGD RKEWHIGVCS KNVQRKGWVK MTPENGFWTM G LTDGNKYR ...String:
EEKKTQFRKK KREQELREMA WSTMKQEQST RVKLLEELRW RSIQYASRGE RHSAYNEWKK ALFKPADVIL DPKTANPILL VSEDQRSVQ RAKEPQDLPD NPERFNWHYC VLGCESFISG RHYWEVEVGD RKEWHIGVCS KNVQRKGWVK MTPENGFWTM G LTDGNKYR TLTEPRTNLK LPKTPKKVGV FLDYETGDIS FYNAVDGSHI HTFLDVSFSE ALYPVFRILT LEPTALTICP A

UniProtKB: Butyrophilin subfamily 3 member A1

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Macromolecule #3: Butyrophilin subfamily 3 member A3

MacromoleculeName: Butyrophilin subfamily 3 member A3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.535941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KEKIALSRET EREREMKEMG YAATEQEISL REKLQEELKW RKIQYMARGE KSLAYHEWKM ALFKPADVIL DPDTANAILL VSEDQRSVQ RAEEPRDLPD NPERFEWRYC VLGCENFTSG RHYWEVEVGD RKEWHIGVCS KNVERKKGWV KMTPENGYWT M GLTDGNKY ...String:
KEKIALSRET EREREMKEMG YAATEQEISL REKLQEELKW RKIQYMARGE KSLAYHEWKM ALFKPADVIL DPDTANAILL VSEDQRSVQ RAEEPRDLPD NPERFEWRYC VLGCENFTSG RHYWEVEVGD RKEWHIGVCS KNVERKKGWV KMTPENGYWT M GLTDGNKY RALTEPRTNL KLPEPPRKVG IFLDYETGEI SFYNATDGSH IYTFPHASFS EPLYPVFRIL TLEPTALTIC PI PKEVESS PDPDLVPDHS LETPLTPGLA NESGEPQAEV TSLLLPAHPG AEVSPSATTN QNHKLQARTE ALY

UniProtKB: Butyrophilin subfamily 3 member A3

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Macromolecule #4: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate

MacromoleculeName: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
type: ligand / ID: 4 / Number of copies: 1 / Formula: H6P
Molecular weightTheoretical: 262.092 Da
Chemical component information

ChemComp-H6P:
(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen 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 K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 449650
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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