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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: To Be Published
Title: Cryo-EM structure of the intracellular domains of BTN2A1-BTN3A1-BTN3A3
Authors: Gao W / Zheng J / Zhu Y / Huang Z
History
DepositionJun 19, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 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
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60591_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 : 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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