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Yorodumi- PDB-8zgt: Structure of the ige-fc bound to its high affinity receptor fc(ep... -
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-Basic information
Entry | Database: PDB / ID: 8zgt | ||||||
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Title | Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state3 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Complex | ||||||
Function / homology | Function and homology information Fc epsilon receptor (FCERI) signaling / Dectin-2 family / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated NF-kB activation / Platelet Adhesion to exposed collagen / IgE receptor activity / Fc-epsilon receptor I complex / serotonin secretion / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall ...Fc epsilon receptor (FCERI) signaling / Dectin-2 family / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated NF-kB activation / Platelet Adhesion to exposed collagen / IgE receptor activity / Fc-epsilon receptor I complex / serotonin secretion / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall / negative regulation of mast cell apoptotic process / FCERI mediated Ca+2 mobilization / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / high-affinity IgE receptor activity / IgE B cell receptor complex / type I hypersensitivity / mast cell apoptotic process / mast cell activation / Fc-gamma receptor III complex / FCERI mediated MAPK activation / positive regulation of interleukin-3 production / positive regulation of mast cell cytokine production / serotonin secretion by platelet / eosinophil degranulation / neutrophil activation involved in immune response / positive regulation of mast cell degranulation / regulation of platelet activation / Fc-gamma receptor signaling pathway / positive regulation of type III hypersensitivity / IgE binding / positive regulation of type IIa hypersensitivity / type 2 immune response / regulation of release of sequestered calcium ion into cytosol / positive regulation of protein localization to cell surface / leukotriene biosynthetic process / : / positive regulation of type I hypersensitivity / interleukin-3-mediated signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / IgG binding / Neutrophil degranulation / mast cell degranulation / phagocytosis, engulfment / positive regulation of interleukin-4 production / antigen processing and presentation of exogenous peptide antigen via MHC class I / Fc-epsilon receptor signaling pathway / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / regulation of immune response / immunoglobulin mediated immune response / positive regulation of phagocytosis / neutrophil chemotaxis / positive regulation of calcium-mediated signaling / SH2 domain binding / B cell differentiation / osteoclast differentiation / establishment of localization in cell / protein localization to plasma membrane / integrin-mediated signaling pathway / phosphoprotein binding / B cell receptor signaling pathway / calcium-mediated signaling / receptor internalization / positive regulation of interleukin-6 production / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / cell surface receptor signaling pathway / endosome / defense response to bacterium / immune response / protein heterodimerization activity / lysosomal membrane / external side of plasma membrane / innate immune response / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å | ||||||
Authors | Du, S. / Deng, M.J. / Xiao, J.Y. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2024 Title: Structural insights into the high-affinity IgE receptor FcεRI complex. Authors: Meijie Deng / Shuo Du / Handi Hou / Junyu Xiao / Abstract: Immunoglobulin E (IgE) plays a pivotal role in allergic responses. The high-affinity IgE receptor, FcεRI, found on mast cells and basophils, is central to the effector functions of IgE. FcεRI is a ...Immunoglobulin E (IgE) plays a pivotal role in allergic responses. The high-affinity IgE receptor, FcεRI, found on mast cells and basophils, is central to the effector functions of IgE. FcεRI is a tetrameric complex, comprising FcεRIα, FcεRIβ and a homodimer of FcRγ (originally known as FcεRIγ), with FcεRIα recognizing the Fc region of IgE (Fcε) and FcεRIβ-FcRγ facilitating signal transduction. Additionally, FcRγ is a crucial component of other immunoglobulin receptors, including those for IgG (FcγRI and FcγRIIIA) and IgA (FcαRI). However, the molecular basis of FcεRI assembly and the structure of FcRγ have remained elusive. Here we elucidate the cryogenic electron microscopy structure of the Fcε-FcεRI complex. FcεRIα has an essential role in the receptor's assembly, interacting with FcεRIβ and both FcRγ subunits. FcεRIβ is structured as a compact four-helix bundle, similar to the B cell antigen CD20. The FcRγ dimer exhibits an asymmetric architecture, and coils with the transmembrane region of FcεRIα to form a three-helix bundle. A cholesterol-like molecule enhances the interaction between FcεRIβ and the FcεRIα-FcRγ complex. Our mutagenesis analyses further indicate similarities between the interaction of FcRγ with FcεRIα and FcγRIIIA, but differences in that with FcαRI. These findings deepen our understanding of the signalling mechanisms of FcεRI and offer insights into the functionality of other immune receptors dependent on FcRγ. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zgt.cif.gz | 240.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zgt.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 8zgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zgt_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8zgt_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8zgt_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 8zgt_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/8zgt ftp://data.pdbj.org/pub/pdb/validation_reports/zg/8zgt | HTTPS FTP |
-Related structure data
Related structure data | 60090MC 8y81C 8y84C 8z0tC 8zgsC 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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-Components
-High affinity immunoglobulin epsilon receptor subunit ... , 3 types, 4 molecules ABCG
#1: Protein | Mass: 27830.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P12371 |
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#2: Protein | Mass: 26747.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P13386 |
#3: Protein | Mass: 9774.509 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P20411 |
-Protein / Non-polymers , 2 types, 3 molecules EF
#4: Protein | Mass: 43155.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: IGHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01855 #8: Chemical | ChemComp-Y01 / | |
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-Sugars , 3 types, 8 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 350802 / Symmetry type: POINT | ||||||||||||||||||||||||
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