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- EMDB-62750: Cryo-EM structure of the ICT01-BTN3A1/BTN3A2 complex, local refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-62750
TitleCryo-EM structure of the ICT01-BTN3A1/BTN3A2 complex, local refinement
Map data
Sample
  • Complex: ICT01-BTN3A1/BTN3A2 complex
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: ICT01 heavy chain
    • Protein or peptide: ICT01 light chain
Keywordsreceptor / antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / signaling receptor binding / external side of plasma membrane / membrane / plasma membrane
Similarity search - Function
: / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Butyrophilin subfamily 3 member A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsXin WZ / Huang BD / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: local refinement of the ICT01-BTN3A1/BTN3A2 complex at 3.7 Angstroms resolution
Authors: Xin WZ / Huang BD / Zhou Q
History
DepositionDec 15, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62750.png

Downloads & links

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Map

FileDownload / File: emd_62750.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 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: 0.5
Minimum - Maximum-4.2564797 - 7.1383514
Average (Standard dev.)-0.0002503671 (±0.062704585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 347.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62750_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62750_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_62750_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 : ICT01-BTN3A1/BTN3A2 complex

EntireName: ICT01-BTN3A1/BTN3A2 complex
Components
  • Complex: ICT01-BTN3A1/BTN3A2 complex
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: ICT01 heavy chain
    • Protein or peptide: ICT01 light chain

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Supramolecule #1: ICT01-BTN3A1/BTN3A2 complex

SupramoleculeName: ICT01-BTN3A1/BTN3A2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Butyrophilin subfamily 3 member A2

MacromoleculeName: Butyrophilin subfamily 3 member A2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.175121 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCQFSVLGPS GPILAMVGED ADLPCHLFPT MSAETMELKW VSSSLRQVVN VYADGKEVED RQSAPYRGR TSILRDGITA GKAALRIHNV TASDSGKYLC YFQDGDFYEK ALVELKVAAL GSNLHVEVKG YEDGGIHLEC R STGWYPQP ...String:
MDMRVPAQLL GLLLLWLSGA RCQFSVLGPS GPILAMVGED ADLPCHLFPT MSAETMELKW VSSSLRQVVN VYADGKEVED RQSAPYRGR TSILRDGITA GKAALRIHNV TASDSGKYLC YFQDGDFYEK ALVELKVAAL GSNLHVEVKG YEDGGIHLEC R STGWYPQP QIQWSNAKGE NIPAVEAPVV ADGVGLYEVA ASVIMRGGSG EGVSCIIRNS LLGLEKTASI SIADPFFRSA QP WIAALAG TLPILLLLLA GASYFLWRQQ KEITALSSEI ESEQEMKEMG YAATEREISL RESLQEELKR KKIQYLTRGE ESS SDTNKS AGSSGMDYKD DDDK

UniProtKB: Butyrophilin subfamily 3 member A2

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Macromolecule #2: ICT01 heavy chain

MacromoleculeName: ICT01 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.789354 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGLSWLFL VAILKGVQCQ VQLVQSGAEV KKPGASVKLS CKASGYIFTR YYMYWVKQRP GQGLEWIGEI NPNNGGTKFN EKFKNRATL TVDKSISTAY MELSRLRSDD TAVYYCSRED DYDGTPFAMD YWGQGTLVTV SSASTKGPSV FPLAPSSKST S GGTAALGC ...String:
MEFGLSWLFL VAILKGVQCQ VQLVQSGAEV KKPGASVKLS CKASGYIFTR YYMYWVKQRP GQGLEWIGEI NPNNGGTKFN EKFKNRATL TVDKSISTAY MELSRLRSDD TAVYYCSRED DYDGTPFAMD YWGQGTLVTV SSASTKGPSV FPLAPSSKST S GGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VE PKSCGGS HHHHHHHH

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Macromolecule #3: ICT01 light chain

MacromoleculeName: ICT01 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.968166 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCDIQMTQSP SSLSASVGDR VTITCHASQN INVWLSWYQQ KPGKAPKLLI YKASNLHTGV PSRFSGSGS GTDFTFTISS LQPEDIATYY CQQGQTYPYT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV ...String:
MDMRVPAQLL GLLLLWLSGA RCDIQMTQSP SSLSASVGDR VTITCHASQN INVWLSWYQQ KPGKAPKLLI YKASNLHTGV PSRFSGSGS GTDFTFTISS LQPEDIATYY CQQGQTYPYT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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: GATAN K3 (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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: PHENIX (ver. 1.20.1), EMAN2 (ver. 2.99.62))
Number images used: 311879
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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