[English] 日本語
Yorodumi
- EMDB-39876: Cryo-EM structure of intracellular HBMBPP-BTN2A1-BTN3A1 complex -

+
Open data


ID or keywords:

Loading...

-
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 / external side of plasma membrane / signaling receptor binding / 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

-
Structure visualization

Supplemental images

emd_39876.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #2

Fileemd_39876_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39876_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
Supramolecule #1: BTN2A1-BTN3A1

SupramoleculeName: BTN2A1-BTN3A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: NITROGEN

-
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

-
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

+
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