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- EMDB-61740: Cryo-EM structure of the Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2... -

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Basic information

Entry
Database: EMDB / ID: EMD-61740
TitleCryo-EM structure of the Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex
Map data
Sample
  • Complex: Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: Vdelta2 T cell receptor
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: Vgamma9 T cell receptor
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsbutyrophilin / phosphoantigen / receptor / 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 / external side of plasma membrane ...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 / external side of plasma membrane / signaling receptor binding / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang M / Wang YQ / Xiao JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32325018 China
CitationJournal: Immunity / Year: 2025
Title: Structures of butyrophilin multimers reveal a plier-like mechanism for V gamma 9V delta 2 T cell receptor activation
Authors: Zhang M / Wang Y / Cai N / Qu Y / Ma X / Xue J / Chen X / Zhang X / Xiao J / Zhang Y
History
DepositionSep 28, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61740.png

Downloads & links

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Map

FileDownload / File: emd_61740.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 420 pix.
= 399. Å		0.95 Å/pix.
x 420 pix.
= 399. Å		0.95 Å/pix.
x 420 pix.
= 399. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.099507846 - 19.268808
Average (Standard dev.)-0.020640997 (±0.33599073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 399.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex

EntireName: Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex
Components
  • Complex: Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: Vdelta2 T cell receptor
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: Vgamma9 T cell receptor
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex

SupramoleculeName: Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.247715 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 GGGGSGGGGS GGGGSWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

UniProtKB: Butyrophilin subfamily 3 member A1

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Macromolecule #2: Butyrophilin subfamily 3 member A2

MacromoleculeName: Butyrophilin subfamily 3 member A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.629918 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QFSVLGPSGP ILAMVGEDAD LPCHLFPTMS AETMELKWVS SSLRQVVNVY ADGKEVEDRQ SAPYRGRTSI LRDGITAGKA ALRIHNVTA SDSGKYLCYF QDGDFYEKAL VELKVAALGS NLHVEVKGYE DGGIHLECRS TGWYPQPQIQ WSNAKGENIP A VEAPVVAD ...String:
QFSVLGPSGP ILAMVGEDAD LPCHLFPTMS AETMELKWVS SSLRQVVNVY ADGKEVEDRQ SAPYRGRTSI LRDGITAGKA ALRIHNVTA SDSGKYLCYF QDGDFYEKAL VELKVAALGS NLHVEVKGYE DGGIHLECRS TGWYPQPQIQ WSNAKGENIP A VEAPVVAD GVGLYEVAAS VIMRGGSGEG VSCIIRNSLL GLEKTASISI ADPFFRSAQP WIAALAGTLP ILLLLLAGAS YF LWRQQKE ITALSSEIES EQEMKEMGYA ATEREISLRE SLQEELKRKK IQYLTRGEES SSDTNKSAGG GGSDYKDDDD K

UniProtKB: Butyrophilin subfamily 3 member A2

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Macromolecule #3: Vdelta2 T cell receptor

MacromoleculeName: Vdelta2 T cell receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.473377 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AIELVPEHQT VPVSIGVPAT LRCSMKGEAI GNYYINWYRK TQGNTMTFIY REKDIYGPGF KDNFQGDIDI AKNLAVLKIL APSERDEGS YYCACDTLGM GGEYTDKLIF GKGTRVTVEP RSQPHTKPSV FVMKNGTNVA CLVKEFYPKD IRINLVSSKK I TEFDPAIV ...String:
AIELVPEHQT VPVSIGVPAT LRCSMKGEAI GNYYINWYRK TQGNTMTFIY REKDIYGPGF KDNFQGDIDI AKNLAVLKIL APSERDEGS YYCACDTLGM GGEYTDKLIF GKGTRVTVEP RSQPHTKPSV FVMKNGTNVA CLVKEFYPKD IRINLVSSKK I TEFDPAIV ISPSGKYNAV KLGKYEDSNS VTCSVQHDNK TVHSTDFEVK TDSTDHVKPK ETENTKQPSK SSSADLVPRG ST TAPSAQL EKELQALEKE NAQLEWELQA LEKELAQ

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Macromolecule #4: Butyrophilin subfamily 2 member A1

MacromoleculeName: Butyrophilin subfamily 2 member A1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.015312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QFIVVGPTDP ILATVGENTT LRCHLSPEKN AEDMEVRWFR SQFSPAVFVY KGGRERTEEQ MEEYRGRTTF VSKDISRGSV ALVIHNITA QENGTYRCYF QEGRSYDEAI LHLVVAGLGS KPLISMRGHE DGGIRLECIS RGWYPKPLTV WRDPYGGVAP A LKEVSMPD ...String:
QFIVVGPTDP ILATVGENTT LRCHLSPEKN AEDMEVRWFR SQFSPAVFVY KGGRERTEEQ MEEYRGRTTF VSKDISRGSV ALVIHNITA QENGTYRCYF QEGRSYDEAI LHLVVAGLGS KPLISMRGHE DGGIRLECIS RGWYPKPLTV WRDPYGGVAP A LKEVSMPD ADGLFMVTTA VIIRDKSVRN MSCSINNTLL GQKKESVIFI PESFMPSVSP CAVALPIIVV ILMIPIAVCI YW INKLQKE KKILSGEKEF ERETREIALK ELEKERVQKE EELQVKEKLQ EELRWRRTFL HAVDVVLDPD TAHPDLFLSE DRR SVRRCP FRHLGESVPD NPERFDSQPC VLGRESFASG KHYWEVEVEN VIEWTVGVCR DSVERKGEVL LIPQNGFWTL EMHK GQYRA VSSPDRILPL KESLCRVGVF LDYEAGDVSF YNMRDRSHIY TCPRSAFSVP VRPFFRLGCE DSPIFICPAL TGANG VTVP EEGLTLHRVG THQSLGGGGS WSHPQFEKGG GSGGGSGGSA WSHPQFEK

UniProtKB: Butyrophilin subfamily 2 member A1

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Macromolecule #5: Vgamma9 T cell receptor

MacromoleculeName: Vgamma9 T cell receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.403363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKFE VDRIPETSTS TLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP SIAETKLQKA GTYLCLLEKF F PDVIKIHW ...String:
AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKFE VDRIPETSTS TLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP SIAETKLQKA GTYLCLLEKF F PDVIKIHW EEKKSNTILG SQEGNTMKTN DTYMKFSWLT VPEKSLDKEH RCIVRHENNK NGVDQEIIFP PIKTDVITMD PK DNSSADL VPRGSTTAPS AQLKKKLQAL KKKNAQLKWK LQALKKKLAQ HHHHHHHH

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Macromolecule #7: (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: 7 / 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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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 1.7 µm / Nominal defocus min: 1.3 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282479
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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