[English] 日本語
Yorodumi
- EMDB-62751: Cryo-EM structure of the ICT01-BTN2A1/BTN3A1/BTN3A2 complex, loca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62751
TitleCryo-EM structure of the ICT01-BTN2A1/BTN3A1/BTN3A2 complex, local refinement
Map data
Sample
  • Complex: ICT01-BTN2A1/BTN3A1/BTN3A2 tetramer complex
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: ICT01 heavy chain
    • Protein or peptide: ICT01 light chain
KeywordsReceptor / IMMUNE SYSTEM
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / lipid metabolic process / 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 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 3 member A2 / Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXin WZ / Huang BD / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100975 China
CitationJournal: To Be Published
Title: Local refinement of the ICT01-BTN2A1/BTN3A1/BTN3A2 complex at 3.7 Angstroms reolution
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

-
Structure visualization

Supplemental images

emd_62751.png

Downloads & links

-
Map

FileDownload / File: emd_62751.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 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: 0.02
Minimum - Maximum-0.16140026 - 0.27259123
Average (Standard dev.)-0.0001198734 (±0.0028956174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62751_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62751_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62751_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ICT01-BTN2A1/BTN3A1/BTN3A2 tetramer complex

EntireName: ICT01-BTN2A1/BTN3A1/BTN3A2 tetramer complex
Components
  • Complex: ICT01-BTN2A1/BTN3A1/BTN3A2 tetramer complex
    • Protein or peptide: Butyrophilin subfamily 2 member A1
    • Protein or peptide: Butyrophilin subfamily 3 member A2
    • Protein or peptide: ICT01 heavy chain
    • Protein or peptide: ICT01 light chain

-
Supramolecule #1: ICT01-BTN2A1/BTN3A1/BTN3A2 tetramer complex

SupramoleculeName: ICT01-BTN2A1/BTN3A1/BTN3A2 tetramer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 272.02 kDa/nm

-
Macromolecule #1: Butyrophilin subfamily 2 member A1

MacromoleculeName: Butyrophilin subfamily 2 member A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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

-
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: 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

-
Macromolecule #3: ICT01 heavy chain

MacromoleculeName: ICT01 heavy chain / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #4: ICT01 light chain

MacromoleculeName: ICT01 light chain / type: protein_or_peptide / ID: 4 / 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

-
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: 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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 354724
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