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- PDB-7xq8: Structure of human B-cell antigen receptor of the IgM isotype -

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Basic information

Entry
Database: PDB / ID: 7xq8
TitleStructure of human B-cell antigen receptor of the IgM isotype
Components
  • B-cell antigen receptor complex-associated protein alpha chain
  • B-cell antigen receptor complex-associated protein beta chain
  • Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu
  • Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant
KeywordsSIGNALING PROTEIN / immunology / B cell signalling / adaptive immunity / antibody
Function / homology
Function and homology information


IgM B cell receptor complex / IgD immunoglobulin complex / B cell receptor complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation ...IgM B cell receptor complex / IgD immunoglobulin complex / B cell receptor complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / B cell activation / immunoglobulin mediated immune response / B cell proliferation / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / multivesicular body / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / B cell differentiation / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / membrane raft / external side of plasma membrane / signal transduction / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 kappa constant / Isoform 2 of 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen, M.Y. / Su, Q. / Shi, Y.G.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81970633 China
National Natural Science Foundation of China (NSFC)U1904146 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: Science / Year: 2022
Title: Cryo-EM structure of the human IgM B cell receptor.
Authors: Qiang Su / Mengying Chen / Yan Shi / Xiaofeng Zhang / Gaoxingyu Huang / Bangdong Huang / Dongwei Liu / Zhangsuo Liu / Yigong Shi /
Abstract: The B cell receptor (BCR) initiates immune responses through antigen recognition. We report a 3.3-angstrom cryo-electron microscopy structure of human immunoglobulin M (IgM)-BCR in the resting state. ...The B cell receptor (BCR) initiates immune responses through antigen recognition. We report a 3.3-angstrom cryo-electron microscopy structure of human immunoglobulin M (IgM)-BCR in the resting state. IgM-BCR comprises two heavy chains, two light chains, and the Igα/Igβ heterodimer. The ectodomains of the heavy chains closely stack against those of Igα/Igβ, with one heavy chain locked between Igα and Igβ in the juxtamembrane region. Extracellular interactions may determine isotype specificity of the BCR. The transmembrane helices of IgM-BCR form a four-helix bundle that appears to be conserved among all BCR isotypes. This structure contains 14 glycosylation sites on the IgM-BCR ectodomains and reveals three potential surface binding sites. Our work reveals the organizational principles of the BCR and may facilitate the design of antibody-based therapeutics.
History
DepositionMay 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.0Aug 17, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Aug 17, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu
L: Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant
v: Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu
R: Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant
A: B-cell antigen receptor complex-associated protein alpha chain
B: B-cell antigen receptor complex-associated protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,89620
Polymers247,7996
Non-polymers3,09714
Water00
1


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

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Components

#1: Antibody Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu / Ig mu chain C region / Ig mu chain C region BOT / Ig mu chain C region GAL / Ig mu chain C region OU


Mass: 67895.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Specific N-terminal secretion signal peptide (1-19)
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01871-2
#2: Antibody Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant


Mass: 27350.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N terminal specific signal peptide (1-19), Flag tag (20-40)
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01834
#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


Mass: 28144.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C terminal twin-strep tag / Source: (gene. exp.) Homo sapiens (human) / Gene: CD79A / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P11912
#4: Protein B-cell antigen receptor complex-associated protein beta chain / B-cell-specific glycoprotein B29 / Ig-beta / Immunoglobulin-associated B29 protein


Mass: 29163.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C terminal twin-strep tag / Source: (gene. exp.) Homo sapiens (human) / Gene: CD79B / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P40259
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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.: 14 / Source method: obtained synthetically / Formula: C8H15NO6
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 interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1structure of human B-cell antigen receptor of the IgM isotypeCOMPLEX#1-#40RECOMBINANT
2Heavy chainCOMPLEX#11RECOMBINANT
3Light chainCOMPLEX#21RECOMBINANT
4human B-cell antigen receptorCOMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Homo sapiens (human)9606
42Homo sapiens (human)9606
52Homo sapiens (human)9606
63Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
11Homo sapiens (human)9606HEK293F
21Homo sapiens (human)9606HEK293F
32Homo sapiens (human)9606HEK293F
42Homo sapiens (human)9606HEK293F
53Homo sapiens (human)9606HEK293F
Buffer solutionpH: 7.5
SpecimenConc.: 5 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 697919 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412656
ELECTRON MICROSCOPYf_angle_d0.59917353
ELECTRON MICROSCOPYf_dihedral_angle_d7.3732038
ELECTRON MICROSCOPYf_chiral_restr0.0482134
ELECTRON MICROSCOPYf_plane_restr0.0052318

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