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- PDB-8ema: mouse full length B cell receptor -

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Basic information

Entry
Database: PDB / ID: 8ema
Titlemouse full length B cell receptor
Components
  • Anti-human Langerin 2G3 lambda chain
  • B-cell antigen receptor complex-associated protein alpha chain
  • B-cell antigen receptor complex-associated protein beta chain
  • Isoform 2 of Immunoglobulin heavy constant mu
KeywordsIMMUNE SYSTEM / COMPLEX / MEMBRANE PROTEIN
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 / immunoglobulin complex / B cell activation / B cell proliferation / 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 / immunoglobulin complex / B cell activation / B cell proliferation / immunoglobulin mediated immune response / multivesicular body / bioluminescence / B cell differentiation / antigen binding / B cell receptor signaling pathway / response to bacterium / transmembrane signaling receptor activity / adaptive immune response / blood microparticle / 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 / 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-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
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)
Aliivibrio fischeri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsYing, D. / Xiong, P. / Michael, R.
Funding support1items
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
DepositionSep 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Immunoglobulin heavy constant mu
B: Isoform 2 of Immunoglobulin heavy constant mu
R: Anti-human Langerin 2G3 lambda chain
L: Anti-human Langerin 2G3 lambda chain
C: B-cell antigen receptor complex-associated protein alpha chain
D: B-cell antigen receptor complex-associated protein beta chain


Theoretical massNumber of molelcules
Total (without water)254,9726
Polymers254,9726
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Isoform 2 of Immunoglobulin heavy constant mu / Ig heavy chain V region VH558 B4


Mass: 68133.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighv1-72, Ighm, Igh-6 / Production host: Mus musculus (house mouse) / References: UniProt: P06328, UniProt: P01872-2
#2: Antibody Anti-human Langerin 2G3 lambda chain


Mass: 25057.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: G0YP42
#3: Protein B-cell antigen receptor complex-associated protein alpha chain / Ig-alpha / MB-1 membrane glycoprotein / Membrane-bound immunoglobulin-associated protein / Surface ...Ig-alpha / MB-1 membrane glycoprotein / Membrane-bound immunoglobulin-associated protein / Surface IgM-associated protein / YFP


Mass: 42837.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Flag-DYKDDDDK Linker: RSIATRS YFP: ...Details: Flag-DYKDDDDK Linker: RSIATRS YFP:MFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW,Flag-DYKDDDDK Linker: RSIATRS YFP:MFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Aliivibrio fischeri (bacteria)
Gene: Cd79a, Iga, Mb-1, luxY / Production host: Mus musculus (house mouse) / References: UniProt: P11911, UniProt: P21578
#4: Protein B-cell antigen receptor complex-associated protein beta chain / B-cell-specific glycoprotein B29 / Ig-beta / Immunoglobulin-associated B29 protein


Mass: 25752.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd79b, Igb / Production host: Mus musculus (house mouse) / References: UniProt: P15530

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: B cell receptor / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30218 / Symmetry type: POINT

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