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Open data
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Basic information
Entry | Database: PDB / ID: 7yte | |||||||||
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Title | crystal structure of human FcmR-D1 bound to IgM C4-domain | |||||||||
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![]() | IMMUNE SYSTEM / FcmR / immunoglobin M | |||||||||
Function / homology | ![]() high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / Fc receptor-mediated immune complex endocytosis / humoral immune response mediated by circulating immunoglobulin / cellular defense response / trans-Golgi network membrane / early endosome membrane ...high-affinity IgM receptor activity / immunoglobulin transcytosis in epithelial cells / IgM binding / regulation of B cell receptor signaling pathway / polymeric immunoglobulin binding / Fc receptor-mediated immune complex endocytosis / humoral immune response mediated by circulating immunoglobulin / cellular defense response / trans-Golgi network membrane / early endosome membrane / lysosomal membrane / negative regulation of apoptotic process / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, Y. / Shen, H. / Xiao, J. | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.9 KB | Display | ![]() |
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PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 450.1 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ysgC ![]() 7ytcC ![]() 7ytdC ![]() 6kxsS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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Components
#1: Protein | Mass: 12452.974 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 11723.567 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1:1 ratio of protein:reservoir solution containing 0.1 M Ammonium citrate tribasic (pH 7.0) and 12% (w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00895 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 9518 / % possible obs: 95.35 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.363 / Num. unique obs: 2435 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KXS Resolution: 3→28.08 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 29.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.44 Å2 / Biso mean: 48.2095 Å2 / Biso min: 20.9 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→28.08 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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