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- EMDB-60172: Cryo-EM structure of pAg-bound BTN2A1-BTN3A1-BTN3A2 in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-60172
TitleCryo-EM structure of pAg-bound BTN2A1-BTN3A1-BTN3A2 in complex with Vgamma9-Vdelta2 TCR (G115 genotype), another TCR focused
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: T cell receptor gamma variable 9,T cell receptor gamma constant 1
KeywordsReceptor / IMMUNE SYSTEM
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / regulation of cytokine production / lipid metabolic process / T cell receptor signaling pathway / signaling receptor binding / external side of plasma membrane / plasma membrane
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY 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 ...Butyrophilin subfamily 1/2, SPRY/PRY 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 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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_60172.png

Downloads & links

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Map

FileDownload / File: emd_60172.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 326.1 Å		1.09 Å/pix.
x 300 pix.
= 326.1 Å		1.09 Å/pix.
x 300 pix.
= 326.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0138
Minimum - Maximum-0.06603306 - 0.11165398
Average (Standard dev.)-0.0003286352 (±0.0022155447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 326.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60172_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60172_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: T cell receptor gamma variable 9,T cell receptor gamma constant 1

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Supramolecule #1: Human BTN complex

SupramoleculeName: Human BTN complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 26.488951 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGAIELVPE HQTVPVSIGV PATLRCSMKG EAIGNYYINW YRKTQGNTMT FIYREKDIYG PGFKDNFQGD IDIAKNLAVL KILAPSERD EGSYYCASDT LGMGGEYTDK LIFGKGTRVT VEPRSQPHTK PSVFVMKNGT NVACLVKEFY PKDIRINLVS S KKITEFDP ...String:
ETGAIELVPE HQTVPVSIGV PATLRCSMKG EAIGNYYINW YRKTQGNTMT FIYREKDIYG PGFKDNFQGD IDIAKNLAVL KILAPSERD EGSYYCASDT LGMGGEYTDK LIFGKGTRVT VEPRSQPHTK PSVFVMKNGT NVACLVKEFY PKDIRINLVS S KKITEFDP AIVISPSGKY NAVKLGKYED SNSVTCSVQH DNKTVHSTDF EVKTDSTDHV KPKETENTKQ PSKSASGLVP R

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.328275 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGAGHLEQP QISSTKTLSK TARLECVVSG ITISATSVYW YRERPGEVIQ FLVSISYDGT VRKESGIPSG KFEVDRIPET STSTLTIHN VEKQDIATYY CALWEAQQEL GKKIKVFGPG TKLIITDKQL DADVSPKPTI FLPSIAETKL QKAGTYLCLL E KFFPDVIK ...String:
ETGAGHLEQP QISSTKTLSK TARLECVVSG ITISATSVYW YRERPGEVIQ FLVSISYDGT VRKESGIPSG KFEVDRIPET STSTLTIHN VEKQDIATYY CALWEAQQEL GKKIKVFGPG TKLIITDKQL DADVSPKPTI FLPSIAETKL QKAGTYLCLL E KFFPDVIK IHWQEKKSNT ILGSQEGNTM KTNDTYMKFS WLTVPEESLD KEHRCIVRHE NNKNGVDQEI IFPPIKTDVI TM DPKDNAS GLVPR

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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: 1999951
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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 164553
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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