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- EMDB-27848: IgM BCR full length -

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Basic information

Entry
Database: EMDB / ID: EMD-27848
TitleIgM BCR full length
Map dataIgM BCR full length
Sample
  • Complex: BCR complex
Function / homology
Function and homology information


CD22 mediated BCR regulation / riboflavin synthase activity / IgM B cell receptor complex / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / riboflavin biosynthetic process / B cell proliferation / B cell activation / immunoglobulin complex / immunoglobulin mediated immune response ...CD22 mediated BCR regulation / riboflavin synthase activity / IgM B cell receptor complex / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / riboflavin biosynthetic process / B cell proliferation / B cell activation / immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / multivesicular body / B cell differentiation / bioluminescence / response to bacterium / B cell receptor signaling pathway / transmembrane signaling receptor activity / adaptive immune response / membrane raft / external side of plasma membrane / extracellular region / identical protein binding / plasma membrane / cytosol
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 / : ...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-Type / 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
Anti-human Langerin 2G3 lambda chain / Isoform 2 of Immunoglobulin heavy constant mu / Ig heavy chain V region 1-72 / 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: 8.2 Å
AuthorsYing D / Xiong P / Hao W / Michael R
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 16, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27848.png

Downloads & links

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Map

FileDownload / File: emd_27848.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIgM BCR full length
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 332 pix.
= 547.8 Å		1.65 Å/pix.
x 332 pix.
= 547.8 Å		1.65 Å/pix.
x 332 pix.
= 547.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.31873724 - 1.7417861
Average (Standard dev.)-0.0010212192 (±0.037726153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 547.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: IgM BCR full length half map A

Fileemd_27848_half_map_1.map
AnnotationIgM BCR full length half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IgM BCR full length half map B

Fileemd_27848_half_map_2.map
AnnotationIgM BCR full length half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BCR complex

EntireName: BCR complex
Components
  • Complex: BCR complex

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Supramolecule #1: BCR complex

SupramoleculeName: BCR complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

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

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Electron microscopy

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

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Image processing

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30218
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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