+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34074 | |||||||||
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Title | Cryo-EM structure of human FcmR bound to sIgM | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / hexameric IgM immunoglobulin complex / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / Fc receptor signaling pathway / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / dimeric IgA immunoglobulin complex ...high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / hexameric IgM immunoglobulin complex / polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / Fc receptor signaling pathway / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / dimeric IgA immunoglobulin complex / IgM B cell receptor complex / 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 / pre-B cell allelic exclusion / detection of chemical stimulus involved in sensory perception of bitter taste / glomerular filtration / IgM immunoglobulin complex / humoral immune response mediated by circulating immunoglobulin / CD22 mediated BCR regulation / azurophil granule membrane / receptor clustering / positive regulation of respiratory burst / humoral immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / trans-Golgi network membrane / cellular defense response / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / antibacterial humoral response / protein-macromolecule adaptor activity / early endosome membrane / protein-containing complex assembly / defense response to Gram-negative bacterium / adaptive immune response / blood microparticle / Potential therapeutics for SARS / receptor complex / immune response / lysosomal membrane / innate immune response / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Li Y / Shen H / Xiao J | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34074.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-34074-v30.xml emd-34074.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_34074.png | 116.8 KB | ||
Others | emd_34074_half_map_1.map.gz emd_34074_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34074 | HTTPS FTP |
-Validation report
Summary document | emd_34074_validation.pdf.gz | 973.6 KB | Display | EMDB validaton report |
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Full document | emd_34074_full_validation.pdf.gz | 973.1 KB | Display | |
Data in XML | emd_34074_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_34074_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34074 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34074 | HTTPS FTP |
-Related structure data
Related structure data | 7ysgMC 7ytcC 7ytdC 7yteC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34074.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34074_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34074_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of human FcmR bound to sIgM
+Supramolecule #1: Cryo-EM structure of human FcmR bound to sIgM
+Supramolecule #2: Immunoglobulin heavy constant mu
+Supramolecule #3: Immunoglobulin J chain
+Supramolecule #4: Secretory component
+Supramolecule #5: Fas apoptotic inhibitory molecule 3
+Macromolecule #1: Immunoglobulin heavy constant mu
+Macromolecule #2: Immunoglobulin J chain
+Macromolecule #3: Secretory component
+Macromolecule #4: Fas apoptotic inhibitory molecule 3
+Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 297136 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |