[English] 日本語
Yorodumi
- EMDB-27888: IgM BCR fab truncated form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27888
TitleIgM BCR fab truncated form
Map dataIgM BCR_Delta_Fab
Sample
  • Complex: BCR complex
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / membrane protein / IMMUNE SYSTEM
Function / homology
Function and homology information


CD22 mediated BCR regulation / hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / positive regulation of B cell activation / B cell affinity maturation ...CD22 mediated BCR regulation / hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / positive regulation of B cell activation / B cell affinity maturation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / regulation of cell morphogenesis / regulation of immunoglobulin production / B cell activation / B cell proliferation / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of B cell proliferation / multivesicular body / bioluminescence / complement activation, classical pathway / B cell differentiation / antigen binding / B cell receptor signaling pathway / response to bacterium / transmembrane signaling receptor activity / positive regulation of immune response / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / antibacterial humoral response / adaptive immune response / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / membrane raft / external side of plasma membrane / innate immune response / perinuclear region of cytoplasm / cell surface / extracellular space / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / 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 ...Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / 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 / ATP synthase subunit alpha, N-terminal domain-like superfamily / Riboflavin synthase-like beta-barrel / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / 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 / Yellow fluorescent protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsDong Y / Pi X / Wu H / Reth M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structural principles of B cell antigen receptor assembly.
Authors: Ying Dong / Xiong Pi / Frauke Bartels-Burgahn / Deniz Saltukoglu / Zhuoyi Liang / Jianying Yang / Frederick W Alt / Michael Reth / Hao Wu /
Abstract: The B cell antigen receptor (BCR) is composed of a membrane-bound class M, D, G, E or A immunoglobulin for antigen recognition and a disulfide-linked Igα (also known as CD79A) and Igβ (also known ...The B cell antigen receptor (BCR) is composed of a membrane-bound class M, D, G, E or A immunoglobulin for antigen recognition and a disulfide-linked Igα (also known as CD79A) and Igβ (also known as CD79B) heterodimer (Igα/β) that functions as the signalling entity through intracellular immunoreceptor tyrosine-based activation motifs (ITAMs). The organizing principle of the BCR remains unknown. Here we report cryo-electron microscopy structures of mouse full-length IgM BCR and its Fab-deleted form. At the ectodomain (ECD), the Igα/β heterodimer mainly uses Igα to associate with Cµ3 and Cµ4 domains of one heavy chain (µHC) while leaving the other heavy chain (µHC') unbound. The transmembrane domain (TMD) helices of µHC and µHC' interact with those of the Igα/β heterodimer to form a tight four-helix bundle. The asymmetry at the TMD prevents the recruitment of two Igα/β heterodimers. Notably, the connecting peptide between the ECD and TMD of µHC intervenes in between those of Igα and Igβ to guide TMD assembly through charge complementarity. Weaker but distinct density for the Igβ ITAM nestles next to the TMD, suggesting potential autoinhibition of ITAM phosphorylation. Interfacial analyses suggest that all BCR classes utilize a general organizational architecture. Our studies provide a structural platform for understanding B cell signalling and designing rational therapies against BCR-mediated diseases.
History
DepositionAug 18, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27888.png

Downloads & links

-
Map

FileDownload / File: emd_27888.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIgM BCR_Delta_Fab
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-3.2019117 - 4.8990765
Average (Standard dev.)0.0010471328 (±0.040835362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 273.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: IgM BCR Delta Fab

Fileemd_27888_half_map_1.map
AnnotationIgM BCR_Delta_Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: IgM BCR Delta Fab

Fileemd_27888_half_map_2.map
AnnotationIgM BCR_Delta_Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BCR complex

EntireName: BCR complex
Components
  • Complex: BCR complex
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: BCR complex

SupramoleculeName: BCR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1
Details: B1-8 leader sequence: MGWSCIILFLVATATGVHS Strep Tag: WSHPQFEK Rigid linker: AEAAAKEAAAKEAAAKA
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 45.753785 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MGWSCIILFL VATATGVHSG GWSHPQFEKA EAAAKEAAAK EAAAKAAVAE MNPNVNVFVP PRDGFSGPAP RKSKLICEAT NFTPKPITV SWLKDGKLVE SGFTTDPVTI ENKGSTPQTY KVISTLTISE IDWLNLNVYT CRVDHRGLTF LKNVSSTCAA S PSTDILTF ...String:
MGWSCIILFL VATATGVHSG GWSHPQFEKA EAAAKEAAAK EAAAKAAVAE MNPNVNVFVP PRDGFSGPAP RKSKLICEAT NFTPKPITV SWLKDGKLVE SGFTTDPVTI ENKGSTPQTY KVISTLTISE IDWLNLNVYT CRVDHRGLTF LKNVSSTCAA S PSTDILTF TIPPSFADIF LSKSANLTCL VSNLATYETL NISWASQSGE PLETKIKIME SHPNGTFSAK GVASVCVEDW NN RKEFVCT VTHRDLPSPQ KKFISKPNEV HKHPPAVYLL PPAREQLNLR ESATVTCLVK GFSPADISVQ WLQRGQLLPQ EKY VTSAPM PEPGAPGFYF THSILTVTEE EWNSGETYTC VVGHEALPHL VTERTVDKST EGEVNAEEEG FENLWTTAST FIVL FLLSL FYSTTVTLFK VK

UniProtKB: Immunoglobulin heavy constant mu

-
Macromolecule #2: B-cell antigen receptor complex-associated protein alpha chain,Ye...

MacromoleculeName: B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
type: protein_or_peptide / ID: 2
Details: Flag tag:DYKDDDDK Linker: RSIATRS,Flag tag:DYKDDDDK Linker: RSIATRS YFP: ...Details: Flag tag:DYKDDDDK Linker: RSIATRS,Flag tag:DYKDDDDK Linker: RSIATRS YFP:MFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW,Flag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 42.83723 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DYKDDDDKMP GGLEALRALP LLLFLSYACL GPGCQALRVE GGPPSLTVNL GEEARLTCEN NGRNPNITWW FSLQSNITWP PVPLGPGQG TTGQLFFPEV NKNHRGLYWC QVIENNILKR SCGTYLRVRN PVPRPFLDMG EGTKNRIITA EGIILLFCAV V PGTLLLFR ...String:
DYKDDDDKMP GGLEALRALP LLLFLSYACL GPGCQALRVE GGPPSLTVNL GEEARLTCEN NGRNPNITWW FSLQSNITWP PVPLGPGQG TTGQLFFPEV NKNHRGLYWC QVIENNILKR SCGTYLRVRN PVPRPFLDMG EGTKNRIITA EGIILLFCAV V PGTLLLFR KRWQNEKFGR SIATRSMFKG IVEGIGIIEK IDIYTDLDKY AIRFPENMLN GIKKESSIMF NGCFLTVTSV NS NIVWFDI FEKEARKLDT FREYKVGDRV NLGTFPKFGA ASGGHILSAR ISCVASIIEI IENEDYQQMW IQIPENFTEF LID KDYIAV DGISLTIDTI KNNQFFISLP LKIAQNTNMK WRKKGDKVNV ELSNKINANQ CW

UniProtKB: B-cell antigen receptor complex-associated protein alpha chain, Yellow fluorescent protein

-
Macromolecule #3: B-cell antigen receptor complex-associated protein beta chain

MacromoleculeName: B-cell antigen receptor complex-associated protein beta chain
type: protein_or_peptide / ID: 3 / Details: full length cd79b / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.752375 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MATLVLSSMP CHWLLFLLLL FSGEPVPAMT SSDLPLNFQG SPCSQIWQHP RFAAKKRSSM VKFHCYTNHS GALTWFRKRG SQQPQELVS EEGRIVQTQN GSVYTLTIQN IQYEDNGIYF CKQKCDSANH NVTDSCGTEL LVLGFSTLDQ LKRRNTLKDG I ILIQTLLI ...String:
MATLVLSSMP CHWLLFLLLL FSGEPVPAMT SSDLPLNFQG SPCSQIWQHP RFAAKKRSSM VKFHCYTNHS GALTWFRKRG SQQPQELVS EEGRIVQTQN GSVYTLTIQN IQYEDNGIYF CKQKCDSANH NVTDSCGTEL LVLGFSTLDQ LKRRNTLKDG I ILIQTLLI ILFIIVPIFL LLDKDDGKAG MEEDHTYEGL NIDQTATYED IVTLRTGEVK WSVGEHPGQE

UniProtKB: B-cell antigen receptor complex-associated protein beta chain

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Details: full length cd79b / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282429

+
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