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- EMDB-39876: Cryo-EM structure of intracellular HBMBPP-BTN2A1-BTN3A1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39876
TitleCryo-EM structure of intracellular HBMBPP-BTN2A1-BTN3A1 complex
Map data
Sample
  • Complex: BTN2A1-BTN3A1
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 2 member A1
  • Ligand: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE
Keywordscomplex / immune / IMMUNE SYSTEM
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / 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 / signaling receptor binding / external side of plasma 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 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZheng J / Gao W / 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 intracellular HBMBPP-BTN2A1-BTN3A1 complex
Authors: Zheng J / Gao W / Zhu Y / Huang Z
History
DepositionApr 24, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39876.png

Downloads & links

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Map

FileDownload / File: emd_39876.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.)
1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.4387317 - 5.2410517
Average (Standard dev.)0.00022216357 (±0.0499404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39876_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39876_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 : BTN2A1-BTN3A1

EntireName: BTN2A1-BTN3A1
Components
  • Complex: BTN2A1-BTN3A1
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: Butyrophilin subfamily 2 member A1
  • Ligand: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE

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Supramolecule #1: BTN2A1-BTN3A1

SupramoleculeName: BTN2A1-BTN3A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.462047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EQELREMAWS TMKQEQSTRV KLLEELRWRS IQYASRGERH SAYNEWKKAL FKPADVILDP KTANPILLVS EDQRSVQRAK EPQDLPDNP ERFNWHYCVL GCESFISGRH YWEVEVGDRK EWHIGVCSKN VQRKGWVKMT PENGFWTMGL TDGNKYRTLT E PRTNLKLP ...String:
EQELREMAWS TMKQEQSTRV KLLEELRWRS IQYASRGERH SAYNEWKKAL FKPADVILDP KTANPILLVS EDQRSVQRAK EPQDLPDNP ERFNWHYCVL GCESFISGRH YWEVEVGDRK EWHIGVCSKN VQRKGWVKMT PENGFWTMGL TDGNKYRTLT E PRTNLKLP KTPKKVGVFL DYETGDISFY NAVDGSHIHT FLDVSFSEAL YPVFRILTLE PTALTICPA

UniProtKB: Butyrophilin subfamily 3 member A1

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Macromolecule #2: Butyrophilin subfamily 2 member A1

MacromoleculeName: Butyrophilin subfamily 2 member A1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.227328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WINKLQKEKK ILSGEKEFER ETREIALKEL EKERVQKEEE LQVKEKLQEE LRWRRTFLHA VDVVLDPDTA HPDLFLSEDR RSVRRCPFR HLGESVPDNP ERFDSQPCVL GRESFASGKH YWEVEVENVI EWTVGVCRDS VERKGEVLLI PQNGFWTLEM H KGQYRAVS ...String:
WINKLQKEKK ILSGEKEFER ETREIALKEL EKERVQKEEE LQVKEKLQEE LRWRRTFLHA VDVVLDPDTA HPDLFLSEDR RSVRRCPFR HLGESVPDNP ERFDSQPCVL GRESFASGKH YWEVEVENVI EWTVGVCRDS VERKGEVLLI PQNGFWTLEM H KGQYRAVS SPDRILPLKE SLCRVGVFLD YEAGDVSFYN MRDRSHIYTC PRSAFSVPVR PFFRLGCEDS PIFICPALTG AN GVTVPEE GLTLHRVGTH QSL

UniProtKB: Butyrophilin subfamily 2 member A1

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Macromolecule #3: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE

MacromoleculeName: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: EIP
Molecular weightTheoretical: 264.107 Da
Chemical component information

ChemComp-EIP:
4-HYDROXY-3-METHYL BUTYL 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 K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 50 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 535747
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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