+Open data
-Basic information
Entry | Database: PDB / ID: 7ytc | ||||||
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Title | Cryo-EM structure of human FcmR bound to IgM-Fc/J | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobin M | ||||||
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 / pre-B cell allelic exclusion / IgM immunoglobulin complex / humoral immune response mediated by circulating immunoglobulin / CD22 mediated BCR regulation / positive regulation of respiratory burst / humoral immune response / cellular defense response / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / trans-Golgi network membrane / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / early endosome membrane / protein-macromolecule adaptor activity / antibacterial humoral response / Potential therapeutics for SARS / protein-containing complex assembly / defense response to Gram-negative bacterium / adaptive immune response / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | ||||||
Authors | Li, Y. / Shen, H. / Xiao, J. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ytc.cif.gz | 422.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ytc.ent.gz | 354.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ytc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/7ytc ftp://data.pdbj.org/pub/pdb/validation_reports/yt/7ytc | HTTPS FTP |
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-Related structure data
Related structure data | 34085MC 7ysgC 7ytdC 7yteC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 25611.771 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01871 #2: Protein | | Mass: 15483.329 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JCHAIN, IGCJ, IGJ / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01591 #3: Protein | | Mass: 11723.567 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCMR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60667 #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 515815 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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