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- PDB-8e4c: IgM BCR fab truncated form -

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Basic information

Entry
Database: PDB / ID: 8e4c
TitleIgM BCR fab truncated form
Components
  • B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
  • 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 / pentameric IgM immunoglobulin complex / B cell receptor complex / Cell surface interactions at the vascular wall / 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 / riboflavin synthase activity / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / Cell surface interactions at the vascular wall / 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 / riboflavin biosynthetic process / regulation of cell morphogenesis / regulation of immunoglobulin production / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell proliferation / B cell activation / antigen processing and presentation / positive regulation of endocytosis / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of B cell proliferation / antigen binding / multivesicular body / B cell differentiation / bioluminescence / response to bacterium / B cell receptor signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / MAPK cascade / transmembrane signaling receptor activity / antibacterial humoral response / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / membrane raft / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / extracellular space / identical protein binding / membrane / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsDong, Y. / Pi, X. / Wu, H. / Reth, M.
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
DepositionAug 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 21, 2022Group: Database references / Category: citation_author / struct_ref_seq_dif
Item: _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.3Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Mar 13, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Revision 1.5Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Isoform 2 of Immunoglobulin heavy constant mu
A: Isoform 2 of Immunoglobulin heavy constant mu
C: B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
D: B-cell antigen receptor complex-associated protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,2039
Polymers160,0974
Non-polymers1,1065
Water00
1


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

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Components

#1: Protein Isoform 2 of Immunoglobulin heavy constant mu


Mass: 45753.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: B1-8 leader sequence: MGWSCIILFLVATATGVHS Strep Tag: WSHPQFEK Rigid linker: AEAAAKEAAAKEAAAKA
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighm, Igh-6 / Production host: Mus musculus (house mouse) / References: UniProt: P01872
#2: Protein B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein / 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 tag:DYKDDDDK Linker: RSIATRS,Flag tag:DYKDDDDK Linker: RSIATRS YFP: ...Details: Flag tag:DYKDDDDK Linker: RSIATRS,Flag tag:DYKDDDDK Linker: RSIATRS YFP:MFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW,Flag
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd79a, Iga, Mb-1, luxY / Production host: Mus musculus (house mouse) / References: UniProt: P11911, UniProt: P21578
#3: 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
Details: full length cd79b / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd79b, Igb / Production host: Mus musculus (house mouse) / References: UniProt: P15530
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / B-cell-specific glycoprotein B29 / Ig-beta / Immunoglobulin-associated B29 protein / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Details: full length cd79b / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: BCR complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenConc.: 0.9 mg/ml / Embedding 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 / Cs: 2.7 mm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282429 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036420
ELECTRON MICROSCOPYf_angle_d0.6538748
ELECTRON MICROSCOPYf_dihedral_angle_d4.19835
ELECTRON MICROSCOPYf_chiral_restr0.043999
ELECTRON MICROSCOPYf_plane_restr0.0051116

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