[English] 日本語
Yorodumi
- EMDB-60811: Cryo-EM structure of BTN2A1-BTN3A1-BTN3A2 mutant (BTN3A1 H381R, B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60811
TitleCryo-EM structure of BTN2A1-BTN3A1-BTN3A2 mutant (BTN3A1 H381R, BTN2A1 R477A/T510A) in complex with Vgamma9-Vdelta2 TCR (G115 genotype)
Map data
Sample
  • Complex: Human BTN tetramer in complex TCR
    • 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: Butyrophilin subfamily 3 member A2
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • 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 / 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 / signaling receptor binding ...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 / signaling receptor binding / external side of plasma membrane / 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 3 member A2 / Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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: To Be Published
Title: Structures of human BTN2A1-BTN3A1-BTN3A2 mutant (BTN3A1 H381R, BTN2A1 R477A/T510A) in complex with Vgamma9-Vdelta2 TCR (G115 genotype) at 3.2 Angstroms resolution
Authors: Xin W / Huang B / Su Q / Zhou Q
History
DepositionJul 15, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60811.png

Downloads & links

-
Map

FileDownload / File: emd_60811.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.)
1.08 Å/pix.
x 360 pix.
= 387.828 Å		1.08 Å/pix.
x 360 pix.
= 387.828 Å		1.08 Å/pix.
x 360 pix.
= 387.828 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: 0.0163
Minimum - Maximum-0.03721223 - 0.09231923
Average (Standard dev.)-0.00008113549 (±0.001477297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 387.82797 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_60811_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60811_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60811_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human BTN tetramer in complex TCR

EntireName: Human BTN tetramer in complex TCR
Components
  • Complex: Human BTN tetramer in complex TCR
    • 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: Butyrophilin subfamily 3 member A2
    • Protein or peptide: Butyrophilin subfamily 3 member A1
    • Protein or peptide: T cell receptor gamma variable 9,T cell receptor gamma constant 1

-
Supramolecule #1: Human BTN tetramer in complex TCR

SupramoleculeName: Human BTN tetramer in complex TCR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
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: 24.037453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QFIVVGPTDP ILATVGENTT LRCHLSPEKN AEDMEVRWFR SQFSPAVFVY KGGRERTEEQ MEEYRGRTTF VSKDISRGSV ALVIHNITA QENGTYRCYF QEGRSYDEAI LHLVVAGLGS KPLISMRGHE DGGIRLECIS RGWYPKPLTV WRDPYGGVAP A LKEVSMPD ...String:
QFIVVGPTDP ILATVGENTT LRCHLSPEKN AEDMEVRWFR SQFSPAVFVY KGGRERTEEQ MEEYRGRTTF VSKDISRGSV ALVIHNITA QENGTYRCYF QEGRSYDEAI LHLVVAGLGS KPLISMRGHE DGGIRLECIS RGWYPKPLTV WRDPYGGVAP A LKEVSMPD ADGLFMVTTA VIIRDKSVRN MSCSINNTLL GQKKESVIFI PESFMP

UniProtKB: Butyrophilin subfamily 2 member A1

-
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: 22.746854 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IELVPEHQTV PVSIGVPATL RCSMKGEAIG NYYINWYRKT QGNTMTFIYR EKDIYGPGFK DNFQGDIDIA KNLAVLKILA PSERDEGSY YCASDTLGMG GEYTDKLIFG KGTRVTVEPR SQPHTKPSVF VMKNGTNVAC LVKEFYPKDI RINLVSSKKI T EFDPAIVI ...String:
IELVPEHQTV PVSIGVPATL RCSMKGEAIG NYYINWYRKT QGNTMTFIYR EKDIYGPGFK DNFQGDIDIA KNLAVLKILA PSERDEGSY YCASDTLGMG GEYTDKLIFG KGTRVTVEPR SQPHTKPSVF VMKNGTNVAC LVKEFYPKDI RINLVSSKKI T EFDPAIVI SPSGKYNAVK LGKYEDSNSV TCSVQHDNKT VHSTDF

-
Macromolecule #3: Butyrophilin subfamily 3 member A2

MacromoleculeName: Butyrophilin subfamily 3 member A2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.904869 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QFSVLGPSGP ILAMVGEDAD LPCHLFPTMS AETMELKWVS SSLRQVVNVY ADGKEVEDRQ SAPYRGRTSI LRDGITAGKA ALRIHNVTA SDSGKYLCYF QDGDFYEKAL VELKVAALGS NLHVEVKGYE DGGIHLECRS TGWYPQPQIQ WSNAKGENIP A VEAPVVAD ...String:
QFSVLGPSGP ILAMVGEDAD LPCHLFPTMS AETMELKWVS SSLRQVVNVY ADGKEVEDRQ SAPYRGRTSI LRDGITAGKA ALRIHNVTA SDSGKYLCYF QDGDFYEKAL VELKVAALGS NLHVEVKGYE DGGIHLECRS TGWYPQPQIQ WSNAKGENIP A VEAPVVAD GVGLYEVAAS VIMRGGSGEG VSCIIRNSLL GLEKTASISI ADPFF

UniProtKB: Butyrophilin subfamily 3 member A2

-
Macromolecule #4: Butyrophilin subfamily 3 member A1

MacromoleculeName: Butyrophilin subfamily 3 member A1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.968932 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AQFSVLGPSG PILAMVGEDA DLPCHLFPTM SAETMELKWV SSSLRQVVNV YADGKEVEDR QSAPYRGRTS ILRDGITAGK AALRIHNVT ASDSGKYLCY FQDGDFYEKA LVELKVAALG SDLHVDVKGY KDGGIHLECR STGWYPQPQI QWSNNKGENI P TVEAPVVA ...String:
AQFSVLGPSG PILAMVGEDA DLPCHLFPTM SAETMELKWV SSSLRQVVNV YADGKEVEDR QSAPYRGRTS ILRDGITAGK AALRIHNVT ASDSGKYLCY FQDGDFYEKA LVELKVAALG SDLHVDVKGY KDGGIHLECR STGWYPQPQI QWSNNKGENI P TVEAPVVA DGVGLYAVAA SVIMRGSSGE GVSCTIRSSL LGLEKTASIS IADPFF

UniProtKB: Butyrophilin subfamily 3 member A1

-
Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.92758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHLEQPQISS TKTLSKTARL ECVVSGITIS ATSVYWYRER PGEVIQFLVS ISYDGTVRKE SGIPSGKFEV DRIPETSTST LTIHNVEKQ DIATYYCALW EAQQELGKKI KVFGPGTKLI ITDKQLDADV SPKPTIFLPS IAETKLQKAG TYLCLLEKFF P DVIKIHWQ ...String:
GHLEQPQISS TKTLSKTARL ECVVSGITIS ATSVYWYRER PGEVIQFLVS ISYDGTVRKE SGIPSGKFEV DRIPETSTST LTIHNVEKQ DIATYYCALW EAQQELGKKI KVFGPGTKLI ITDKQLDADV SPKPTIFLPS IAETKLQKAG TYLCLLEKFF P DVIKIHWQ EKKSNTILGS QEGNTMKTND TYMKFSWLTV PEESLDKEHR CIVRHENNKN GVDQEIIFPP I

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 524257
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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