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- EMDB-60160: Cryo-EM structure of pAg-bound BTN2A1-BTN3A1-BTN3A3 in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-60160
TitleCryo-EM structure of pAg-bound BTN2A1-BTN3A1-BTN3A3 in complex with Vgamma9-Vdelta2 TCR (G115 genotype)
Map data
Sample
  • Complex: Human BTN complex
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: T cell receptor delta variable 2, T cell receptor delta constant 1
    • Protein or peptide: Butyrophilin subfamily 3 member A3
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: T cell receptor gamma variable 9, T cell receptor gamma constant 1
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
KeywordsReceptor / 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: 3.7 Å
AuthorsXin W / Huang B / Su Q / Zhou Q
Funding support China, 1 items
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, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60160.png

Downloads & links

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Map

FileDownload / File: emd_60160.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 400 pix.
= 434.8 Å		1.09 Å/pix.
x 400 pix.
= 434.8 Å		1.09 Å/pix.
x 400 pix.
= 434.8 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00386
Minimum - Maximum-0.011588788 - 0.029699279
Average (Standard dev.)0.0000015591738 (±0.0005802027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 434.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60160_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60160_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60160_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human BTN complex

EntireName: Human BTN complex
Components
  • Complex: Human BTN complex
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: T cell receptor delta variable 2, T cell receptor delta constant 1
    • Protein or peptide: Butyrophilin subfamily 3 member A3
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: T cell receptor gamma variable 9, T cell receptor gamma constant 1
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate

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Supramolecule #1: Human BTN complex

SupramoleculeName: Human BTN complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 213 kDa/nm

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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: 60.684453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCQFIVVGPT DPILATVGEN TTLRCHLSPE KNAEDMEVRW FRSQFSPAVF VYKGGRERTE EQMEEYRGR TTFVSKDISR GSVALVIHNI TAQENGTYRC YFQEGRSYDE AILHLVVAGL GSKPLISMRG HEDGGIRLEC I SRGWYPKP ...String:
MDMRVPAQLL GLLLLWLSGA RCQFIVVGPT DPILATVGEN TTLRCHLSPE KNAEDMEVRW FRSQFSPAVF VYKGGRERTE EQMEEYRGR TTFVSKDISR GSVALVIHNI TAQENGTYRC YFQEGRSYDE AILHLVVAGL GSKPLISMRG HEDGGIRLEC I SRGWYPKP LTVWRDPYGG VAPALKEVSM PDADGLFMVT TAVIIRDKSV RNMSCSINNT LLGQKKESVI FIPESFMPSV SP CAVALPI IVVILMIPIA VCIYWINKLQ KEKKILSGEK EFERETREIA LKELEKERVQ KEEELQVKEK LQEELRWRRT FLH AVDVVL DPDTAHPDLF LSEDRRSVRR CPFRHLGESV PDNPERFDSQ PCVLGRESFA SGKHYWEVEV ENVIEWTVGV CRDS VERKG EVLLIPQNGF WTLEMHKGQY RAVSSPDRIL PLKESLCRVG VFLDYEAGDV SFYNMRDRSH IYTCPRSAFS VPVRP FFRL GCEDSPIFIC PALTGANGVT VPEEGLTLHR VGTHQSLGSS GMDYKDDDDK

UniProtKB: Butyrophilin subfamily 2 member A1

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

MacromoleculeName: T cell receptor delta variable 2, T cell receptor delta constant 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.746854 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IELVPEHQTV PVSIGVPATL RCSMKGEAIG NYYINWYRKT QGNTMTFIYR EKDIYGPGFK DNFQGDIDIA KNLAVLKILA PSERDEGSY YCASDTLGMG GEYTDKLIFG KGTRVTVEPR SQPHTKPSVF VMKNGTNVAC LVKEFYPKDI RINLVSSKKI T EFDPAIVI ...String:
IELVPEHQTV PVSIGVPATL RCSMKGEAIG NYYINWYRKT QGNTMTFIYR EKDIYGPGFK DNFQGDIDIA KNLAVLKILA PSERDEGSY YCASDTLGMG GEYTDKLIFG KGTRVTVEPR SQPHTKPSVF VMKNGTNVAC LVKEFYPKDI RINLVSSKKI T EFDPAIVI SPSGKYNAVK LGKYEDSNSV TCSVQHDNKT VHSTDF

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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: 65.729406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCQFSVLGPS GPILAMVGED ADLPCHLFPT MSAETMELRW VSSSLRQVVN VYADGKEVED RQSAPYRGR TSILRDGITA GKAALRIHNV TASDSGKYLC YFQDGDFYEK ALVELKVAAL GSDLHIEVKG YEDGGIHLEC R STGWYPQP ...String:
MDMRVPAQLL GLLLLWLSGA RCQFSVLGPS GPILAMVGED ADLPCHLFPT MSAETMELRW VSSSLRQVVN VYADGKEVED RQSAPYRGR TSILRDGITA GKAALRIHNV TASDSGKYLC YFQDGDFYEK ALVELKVAAL GSDLHIEVKG YEDGGIHLEC R STGWYPQP QIKWSDTKGE NIPAVEAPVV ADGVGLYAVA ASVIMRGSSG GGVSCIIRNS LLGLEKTASI SIADPFFRSA QP WIAALAG TLPISLLLLA GASYFLWRQQ KEKIALSRET EREREMKEMG YAATEQEISL REKLQEELKW RKIQYMARGE KSL AYHEWK MALFKPADVI LDPDTANAIL LVSEDQRSVQ RAEEPRDLPD NPERFEWRYC VLGCENFTSG RHYWEVEVGD RKEW HIGVC SKNVERKKGW VKMTPENGYW TMGLTDGNKY RALTEPRTNL KLPEPPRKVG IFLDYETGEI SFYNATDGSH IYTFP HASF SEPLYPVFRI LTLEPTALTI CPIPKEVESS PDPDLVPDHS LETPLTPGLA NESGEPQAEV TSLLLPAHPG AEVSPS ATT NQNHKLQART EALYGSSGHH HHHHHH

UniProtKB: Butyrophilin subfamily 3 member A3

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Macromolecule #4: Butyrophilin subfamily 3 member A1

MacromoleculeName: Butyrophilin subfamily 3 member A1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.42882 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QFSVLGPSGP ILAMVGEDAD LPCHLFPTMS AETMELKWVS SSLRQVVNVY ADGKEVEDRQ SAPYRGRTSI LRDGITAGKA ALRIHNVTA SDSGKYLCYF QDGDFYEKAL VELKVAALGS DLHVDVKGYK DGGIHLECRS TGWYPQPQIQ WSNNKGENIP T VEAPVVAD ...String:
QFSVLGPSGP ILAMVGEDAD LPCHLFPTMS AETMELKWVS SSLRQVVNVY ADGKEVEDRQ SAPYRGRTSI LRDGITAGKA ALRIHNVTA SDSGKYLCYF QDGDFYEKAL VELKVAALGS DLHVDVKGYK DGGIHLECRS TGWYPQPQIQ WSNNKGENIP T VEAPVVAD GVGLYAVAAS VIMRGSSGEG VSCTIRSSLL GLEKTASISI ADPFFRSAQR WIAALAGTLP VLLLLLGGAG YF LWQQQEE KKTQFRKKKR EQELREMAWS TMKQEQSTRV KLLEELRWRS IQYASRGERH SAYNEWKKAL FKPADVILDP KTA NPILLV SEDQRSVQRA KEPQDLPDNP ERFNWHYCVL GCESFISGRH YWEVEVGDRK EWHIGVCSKN VQRKGWVKMT PENG FWTMG LTDGNKYRTL TEPRTNLKLP KPPKKVGVFL DYETGDISFY NAVDGSHIHT FLDVSFSEAL YPVFRILTLE PTALT ICPA

UniProtKB: Butyrophilin subfamily 3 member A1

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Macromolecule #5: T cell receptor gamma variable 9, T cell receptor gamma constant 1

MacromoleculeName: T cell receptor gamma variable 9, T cell receptor gamma constant 1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.92758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHLEQPQISS TKTLSKTARL ECVVSGITIS ATSVYWYRER PGEVIQFLVS ISYDGTVRKE SGIPSGKFEV DRIPETSTST LTIHNVEKQ DIATYYCALW EAQQELGKKI KVFGPGTKLI ITDKQLDADV SPKPTIFLPS IAETKLQKAG TYLCLLEKFF P DVIKIHWQ ...String:
GHLEQPQISS TKTLSKTARL ECVVSGITIS ATSVYWYRER PGEVIQFLVS ISYDGTVRKE SGIPSGKFEV DRIPETSTST LTIHNVEKQ DIATYYCALW EAQQELGKKI KVFGPGTKLI ITDKQLDADV SPKPTIFLPS IAETKLQKAG TYLCLLEKFF P DVIKIHWQ EKKSNTILGS QEGNTMKTND TYMKFSWLTV PEESLDKEHR CIVRHENNKN GVDQEIIFPP I

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Macromolecule #6: (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: 6 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1023733
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 413213
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)

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