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- EMDB-34086: Cryo-EM structure of four human FcmR bound to IgM-Fc/J -

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Basic information

Entry
Database: EMDB / ID: EMD-34086
TitleCryo-EM structure of four human FcmR bound to IgM-Fc/J
Map data
Sample
  • Complex: Cryo-EM structure of four human FcmR bound to IgM-Fc/J
    • Complex: Immunoglobulin heavy constant mu
      • Protein or peptide: Immunoglobulin heavy constant mu
    • Complex: Immunoglobulin J chain
      • Protein or peptide: Immunoglobulin J chain
    • Complex: FcmR
      • Protein or peptide: Fas apoptotic inhibitory molecule 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / hexameric IgM immunoglobulin complex / regulation of B cell receptor signaling pathway / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / polymeric immunoglobulin binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex ...high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / hexameric IgM immunoglobulin complex / regulation of B cell receptor signaling pathway / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / polymeric immunoglobulin binding / secretory dimeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / Fc receptor-mediated immune complex endocytosis / IgA binding / glomerular filtration / IgM immunoglobulin complex / pre-B cell allelic exclusion / humoral immune response mediated by circulating immunoglobulin / CD22 mediated BCR regulation / positive regulation of respiratory burst / humoral immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / cellular defense response / Scavenging of heme from plasma / complement activation, classical pathway / trans-Golgi network membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / protein-macromolecule adaptor activity / early endosome membrane / antibacterial humoral response / protein-containing complex assembly / adaptive immune response / defense response to Gram-negative bacterium / Potential therapeutics for SARS / blood microparticle / immune response / lysosomal membrane / innate immune response / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin J chain / Immunoglobulin J chain / 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 J chain / Immunoglobulin J chain / 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 mu Fc receptor / Immunoglobulin J chain / Immunoglobulin heavy constant mu
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsLi Y / Shen H / Xiao J
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nature / Year: 2023
Title: Immunoglobulin M perception by FcμR.
Authors: Yaxin Li / Hao Shen / Ruixue Zhang / Chenggong Ji / Yuxin Wang / Chen Su / Junyu Xiao /
Abstract: Immunoglobulin M (IgM) is the first antibody to emerge during embryonic development and the humoral immune response. IgM can exist in several distinct forms, including monomeric, membrane-bound IgM ...Immunoglobulin M (IgM) is the first antibody to emerge during embryonic development and the humoral immune response. IgM can exist in several distinct forms, including monomeric, membrane-bound IgM within the B cell receptor (BCR) complex, pentameric and hexameric IgM in serum and secretory IgM on the mucosal surface. FcμR, the only IgM-specific receptor in mammals, recognizes different forms of IgM to regulate diverse immune responses. However, the underlying molecular mechanisms remain unknown. Here we delineate the structural basis of the FcμR-IgM interaction by crystallography and cryo-electron microscopy. We show that two FcμR molecules interact with a Fcμ-Cμ4 dimer, suggesting that FcμR can bind to membrane-bound IgM with a 2:1 stoichiometry. Further analyses reveal that FcμR-binding sites are accessible in the context of IgM BCR. By contrast, pentameric IgM can recruit four FcμR molecules to bind on the same side and thereby facilitate the formation of an FcμR oligomer. One of these FcμR molecules occupies the binding site of the secretory component. Nevertheless, four FcμR molecules bind to the other side of secretory component-containing secretory IgM, consistent with the function of FcμR in the retrotransport of secretory IgM. These results reveal intricate mechanisms of IgM perception by FcμR.
History
DepositionAug 14, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34086.png

Downloads & links

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Map

FileDownload / File: emd_34086.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.47569755 - 0.9393691
Average (Standard dev.)0.0064265677 (±0.030054264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34086_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_34086_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of four human FcmR bound to IgM-Fc/J

EntireName: Cryo-EM structure of four human FcmR bound to IgM-Fc/J
Components
  • Complex: Cryo-EM structure of four human FcmR bound to IgM-Fc/J
    • Complex: Immunoglobulin heavy constant mu
      • Protein or peptide: Immunoglobulin heavy constant mu
    • Complex: Immunoglobulin J chain
      • Protein or peptide: Immunoglobulin J chain
    • Complex: FcmR
      • Protein or peptide: Fas apoptotic inhibitory molecule 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of four human FcmR bound to IgM-Fc/J

SupramoleculeName: Cryo-EM structure of four human FcmR bound to IgM-Fc/J
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Immunoglobulin heavy constant mu

SupramoleculeName: Immunoglobulin heavy constant mu / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Immunoglobulin J chain

SupramoleculeName: Immunoglobulin J chain / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: FcmR

SupramoleculeName: FcmR / type: complex / ID: 4 / Chimera: Yes / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: Immunoglobulin heavy constant mu

MacromoleculeName: Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.448598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IRVFAIPPSF ASIFLTKSTK LTCLVTDLTT YDSVTISWTR QNGEAVKTHT NISESHPNAT FSAVGEASIC EDDWNSGERF TCTVTHTDL PSPLKQTISR PKGVALHRPD VYLLPPAREQ LNLRESATIT CLVTGFSPAD VFVQWMQRGQ PLSPEKYVTS A PMPEPQAP ...String:
IRVFAIPPSF ASIFLTKSTK LTCLVTDLTT YDSVTISWTR QNGEAVKTHT NISESHPNAT FSAVGEASIC EDDWNSGERF TCTVTHTDL PSPLKQTISR PKGVALHRPD VYLLPPAREQ LNLRESATIT CLVTGFSPAD VFVQWMQRGQ PLSPEKYVTS A PMPEPQAP GRYFAHSILT VSEEEWNTGE TYTCVVAHEA LPNRVTERTV DKSTGKPTLY NVSLVMSDTA GTC

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Macromolecule #2: Immunoglobulin J chain

MacromoleculeName: Immunoglobulin J chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.483329 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EDERIVLVDN KCKCARITSR IIRSSEDPNE DIVERNIRII VPLNNRENIS DPTSPLRTRF VYHLSDLCKK CDPTEVELDN QIVTATQSN ICDEDSATET CYTYDRNKCY TAVVPLVYGG ETKMVETALT PDACYPD

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Macromolecule #3: Fas apoptotic inhibitory molecule 3

MacromoleculeName: Fas apoptotic inhibitory molecule 3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.723567 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
RILPEVKVEG ELGGSVTIKC PLPEMHVRIY LCREMAGSGT CGTVVSTTNF IKAEYKGRVT LKQYPRKNLF LVEVTQLTES DSGVYACGA GMNTDRGKTQ KVTLNVHS

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 10 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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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: 1.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kxs

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 202159

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