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- EMDB-33390: Structure of human B-cell antigen receptor of the IgM isotype -

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Basic information

Entry
Database: EMDB / ID: EMD-33390
TitleStructure of human B-cell antigen receptor of the IgM isotype
Map data
Sample
  • Complex: structure of human B-cell antigen receptor of the IgM isotype
    • Complex: Heavy chain
      • Protein or peptide: Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu
    • Complex: Light chain
      • Protein or peptide: Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant
    • Complex: human B-cell antigen receptor
      • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
      • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


IgM B cell receptor complex / IgD immunoglobulin complex / B cell receptor complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement ...IgM B cell receptor complex / IgD immunoglobulin complex / B cell receptor complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / B cell activation / IgG immunoglobulin complex / B cell proliferation / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / multivesicular body / FCERI mediated Ca+2 mobilization / B cell differentiation / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / 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
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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen MY / Su Q / Shi YG
Funding support China, 4 items
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, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33390.png

Downloads & links

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Map

FileDownload / File: emd_33390.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.077 Å
Density
Contour LevelBy AUTHOR: 0.904
Minimum - Maximum-4.5344486 - 7.251618
Average (Standard dev.)-0.0010767624 (±0.06641249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 387.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33390_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33390_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : structure of human B-cell antigen receptor of the IgM isotype

EntireName: structure of human B-cell antigen receptor of the IgM isotype
Components
  • Complex: structure of human B-cell antigen receptor of the IgM isotype
    • Complex: Heavy chain
      • Protein or peptide: Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu
    • Complex: Light chain
      • Protein or peptide: Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant
    • Complex: human B-cell antigen receptor
      • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
      • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: structure of human B-cell antigen receptor of the IgM isotype

SupramoleculeName: structure of human B-cell antigen receptor of the IgM isotype
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #2: Heavy chain

SupramoleculeName: Heavy chain / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #3: Light chain

SupramoleculeName: Light chain / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #4: human B-cell antigen receptor

SupramoleculeName: human B-cell antigen receptor / type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #3-#4

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Macromolecule #1: Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Imm...

MacromoleculeName: Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu
type: protein_or_peptide / ID: 1
Details: Specific N-terminal secretion signal peptide (1-19)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.895641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGLSWLFL VAILKGVQCQ VQLVQSGGQM KKPGESMRIS CRASGYEFID CTLNWIRLAP GKRPEWMGWL KPRGGAVNYA RPLQGRVTM TRDVYSDTAF LELRSLTVDD TAVYFCTRGK NCDYNWDFEH WGRGTPVIVS SGSASAPTLF PLVSCENSPS D TSSVAVGC ...String:
MEFGLSWLFL VAILKGVQCQ VQLVQSGGQM KKPGESMRIS CRASGYEFID CTLNWIRLAP GKRPEWMGWL KPRGGAVNYA RPLQGRVTM TRDVYSDTAF LELRSLTVDD TAVYFCTRGK NCDYNWDFEH WGRGTPVIVS SGSASAPTLF PLVSCENSPS D TSSVAVGC LAQDFLPDSI TFSWKYKNNS DISSTRGFPS VLRGGKYAAT SQVLLPSKDV MQGTDEHVVC KVQHPNGNKE KN VPLPVIA ELPPKVSVFV PPRDGFFGNP RKSKLICQAT GFSPRQIQVS WLREGKQVGS GVTTDQVQAE AKESGPTTYK VTS TLTIKE SDWLGQSMFT CRVDHRGLTF QQNASSMCVP DQDTAIRVFA IPPSFASIFL TKSTKLTCLV TDLTTYDSVT ISWT RQNGE AVKTHTNISE SHPNATFSAV GEASICEDDW NSGERFTCTV THTDLPSPLK QTISRPKGVA LHRPDVYLLP PAREQ LNLR ESATITCLVT GFSPADVFVQ WMQRGQPLSP EKYVTSAPMP EPQAPGRYFA HSILTVSEEE WNTGETYTCV VAHEAL PNR VTERTVDKST EGEVSADEEG FENLWATAST FIVLFLLSLF YSTTVTLFKV K

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Macromolecule #2: Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin...

MacromoleculeName: Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant
type: protein_or_peptide / ID: 2
Details: N terminal specific signal peptide (1-19), Flag tag (20-40)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.350191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLQTQVFIS LLLWISGAYG GSDYKDDDDK GSPGDEVDAG EIVLTQSPGT LSLSPGETAI ISCRTSQYGS LAWYQQRPGQ APRLVIYSG STRAAGIPDR FSGSRWGPDY NLTISNLESG DFGVYYCQQY EFFGQGTKVQ VDIKRTVAAP SVFIFPPSDE Q LKSGTASV ...String:
MVLQTQVFIS LLLWISGAYG GSDYKDDDDK GSPGDEVDAG EIVLTQSPGT LSLSPGETAI ISCRTSQYGS LAWYQQRPGQ APRLVIYSG STRAAGIPDR FSGSRWGPDY NLTISNLESG DFGVYYCQQY EFFGQGTKVQ VDIKRTVAAP SVFIFPPSDE Q LKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SP VTKSFNR GEC

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

MacromoleculeName: B-cell antigen receptor complex-associated protein alpha chain
type: protein_or_peptide / ID: 3 / Details: C terminal twin-strep tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.144594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPGGPGVLQA LPATIFLLFL LSAVYLGPGC QALWMHKVPA SLMVSLGEDA HFQCPHNSSN NANVTWWRVL HGNYTWPPEF LGPGEDPNG TLIIQNVNKS HGGIYVCRVQ EGNESYQQSC GTYLRVRQPP PRPFLDMGEG TKNRIITAEG IILLFCAVVP G TLLLFRKR ...String:
MPGGPGVLQA LPATIFLLFL LSAVYLGPGC QALWMHKVPA SLMVSLGEDA HFQCPHNSSN NANVTWWRVL HGNYTWPPEF LGPGEDPNG TLIIQNVNKS HGGIYVCRVQ EGNESYQQSC GTYLRVRQPP PRPFLDMGEG TKNRIITAEG IILLFCAVVP G TLLLFRKR WQNEKLGLDA GDEYEDENLY EGLNLDDCSM YEDISRGLQG TYQDVGSLNI GDVQLEKPAA AWSHPQFEKG GG SGGGSGG SAWSHPQFEK

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Macromolecule #4: B-cell antigen receptor complex-associated protein beta chain

MacromoleculeName: B-cell antigen receptor complex-associated protein beta chain
type: protein_or_peptide / ID: 4 / Details: C terminal twin-strep tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.163094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARLALSPVP SHWMVALLLL LSAEPVPAAR SEDRYRNPKG SACSRIWQSP RFIARKRGFT VKMHCYMNSA SGNVSWLWKQ EMDENPQQL KLEKGRMEES QNESLATLTI QGIRFEDNGI YFCQQKCNNT SEVYQGCGTE LRVMGFSTLA QLKQRNTLKD G IIMIQTLL ...String:
MARLALSPVP SHWMVALLLL LSAEPVPAAR SEDRYRNPKG SACSRIWQSP RFIARKRGFT VKMHCYMNSA SGNVSWLWKQ EMDENPQQL KLEKGRMEES QNESLATLTI QGIRFEDNGI YFCQQKCNNT SEVYQGCGTE LRVMGFSTLA QLKQRNTLKD G IIMIQTLL IILFIIVPIF LLLDKDDSKA GMEEDHTYEG LDIDQTATYE DIVTLRTGEV KWSVGEHPGQ EAAAWSHPQF EK GGGSGGG SGGSAWSHPQ FEK

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 14 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 697919

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