[English] 日本語
Yorodumi
- EMDB-61736: Cryo-EM structure of the HMBPP-primed BTN3A1-BTN3A2-BTN2A1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61736
TitleCryo-EM structure of the HMBPP-primed BTN3A1-BTN3A2-BTN2A1 complex
Map data
Sample
  • Complex: HMBPP-primed BTN3A1-BTN3A2-BTN2A1 tetramer complex
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: Butyrophilin subfamily 2 member A1
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsphosphoantigen / butyrophilin / 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: 3.26 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 Vγ9Vδ2 T cell receptor activation.
Authors: Mai Zhang / Yiqing Wang / Ningning Cai / Yingying Qu / Xianqiang Ma / Jing Xue / Xiaorui Chen / Xueguang Zhang / Junyu Xiao / Yonghui Zhang /
Abstract: Vγ9Vδ2 T cells, the major circulating human γδ T cell subset, respond to infections and tumors by recognizing phosphoantigens (pAgs) via transmembrane butyrophilins (BTN3A1, BTN3A2, and BTN2A1). ...Vγ9Vδ2 T cells, the major circulating human γδ T cell subset, respond to infections and tumors by recognizing phosphoantigens (pAgs) via transmembrane butyrophilins (BTN3A1, BTN3A2, and BTN2A1). Here, using cryoelectron microscopy, we resolved the structures of BTN multimers bound to the microbial pAg HMBPP alone and in complex with the T cell receptor (TCR). These structures reveal that BTN3A1 and BTN2A1 cooperate to sense pAgs through their intracellular B30.2 domains, whereas BTN3A2 and BTN2A1 interact extracellularly. TCR engagement triggers its conformational changes, allowing BTN2A1 to bind the Vγ9 chain laterally and BTN3A2 to interact apically with the Vδ2 chain's germline-encoded regions and CDR3 motif, as well as the Vγ9 CDR3. Our study uncovers a "plier-like gripping" mechanism, where BTN multimers bridge the TCR surface to drive activation. These findings establish a structural foundation for γδ T cell-targeted immunotherapies distinct from αβ T cell strategies reliant on major-histocompatibility-complex-mediated antigen presentation.
History
DepositionSep 28, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61736.png

Downloads & links

-
Map

FileDownload / File: emd_61736.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-0.099525124 - 15.7316675
Average (Standard dev.)-0.025637884 (±0.28651083)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: #1

Fileemd_61736_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HMBPP-primed BTN3A1-BTN3A2-BTN2A1 tetramer complex

EntireName: HMBPP-primed BTN3A1-BTN3A2-BTN2A1 tetramer complex
Components
  • Complex: HMBPP-primed BTN3A1-BTN3A2-BTN2A1 tetramer complex
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: Butyrophilin subfamily 2 member A1
  • Ligand: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: HMBPP-primed BTN3A1-BTN3A2-BTN2A1 tetramer complex

SupramoleculeName: HMBPP-primed BTN3A1-BTN3A2-BTN2A1 tetramer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
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

-
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

-
Macromolecule #3: Butyrophilin subfamily 2 member A1

MacromoleculeName: Butyrophilin subfamily 2 member A1 / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #5: (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: 5 / 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

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 264215
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more