[English] 日本語
Yorodumi
- EMDB-32763: Structure of a membrane protein M -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32763
TitleStructure of a membrane protein M
Map data
Sample
  • Complex: complex
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
Function / homology
Function and homology information


hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / IgM immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / B cell activation / B cell proliferation / immunoglobulin complex, circulating ...hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / IgM immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / B cell activation / B cell proliferation / immunoglobulin complex, circulating / immunoglobulin receptor binding / multivesicular body / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Cell surface interactions at the vascular wall / antigen binding / B cell receptor signaling pathway / transmembrane signaling receptor activity / antibacterial humoral response / adaptive immune response / Potential therapeutics for SARS / defense response to Gram-negative bacterium / blood microparticle / immune response / membrane raft / external side of plasma membrane / innate immune response / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...B-cell antigen receptor complex-associated protein alpha/beta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant mu / B-cell antigen receptor complex-associated protein alpha chain / B-cell antigen receptor complex-associated protein beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.09 Å
AuthorsMa X / Zhu Y / Chen Y / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of a membrane protein M
Authors: Ma X / Zhu Y / Chen Y / Huang Z
History
DepositionJan 30, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32763.png

Downloads & links

-
Map

FileDownload / File: emd_32763.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.347
Minimum - Maximum-1.6982644 - 2.6934707
Average (Standard dev.)0.0025124988 (±0.055152643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : complex

EntireName: complex
Components
  • Complex: complex
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu

-
Supramolecule #1: complex

SupramoleculeName: complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: B-cell antigen receptor complex-associated protein alpha chain

MacromoleculeName: B-cell antigen receptor complex-associated protein alpha chain
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.504718 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LWMHKVPASL MVSLGEDAHF QCPHNSSNNA NVTWWRVLHG NYTWPPEFLG PGEDPNGTLI IQNVNKSHGG IYVCRVQEGN ESYQQSCGT YLRVRQPPPR PFLDMGEGTK NRIITAEGII LLFCAVVPGT LLLFRKRW

-
Macromolecule #2: B-cell antigen receptor complex-associated protein beta chain

MacromoleculeName: B-cell antigen receptor complex-associated protein beta chain
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.143744 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SRIWQSPRFI ARKRGFTVKM HCYMNSASGN VSWLWKQEMD ENPQQLKLEK GRMEESQNES LATLTIQGIR FEDNGIYFCQ QKCNNTSEV YQGCGTELRV MGFSTLAQLK QRNTLKDGII MIQTLLIILF IIVPIFLLLD

-
Macromolecule #3: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.470355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI ...String:
IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI SESHPNATFS AVGEASICED DWNSGERFTC TVTHTDLPSP LKQTISRPKG VALHRPDVYL LPPAREQLNL RE SATITCL VTGFSPADVF VQWMQRGQPL SPEKYVTSAP MPEPQAPGRY FAHSILTVSE EEWNTGETYT CVVAHEALPN RVT ERTVDK STEGEVSADE EGFENLWATA STFIVLFLLS LFYSTTVTLF

-
Macromolecule #4: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.599535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI ...String:
IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI SESHPNATFS AVGEASICED DWNSGERFTC TVTHTDLPSP LKQTISRPKG VALHRPDVYL LPPAREQLNL RE SATITCL VTGFSPADVF VQWMQRGQPL SPEKYVTSAP MPEPQAPGRY FAHSILTVSE EEWNTGETYT CVVAHEALPN RVT ERTVDK STEGEVSADE EGFENLWATA STFIVLFLLS LFYSTTVTLF K

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7k0c

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47428
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://pdbjlvh1.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