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Yorodumi- PDB-8y81: Structure of the ige-fc bound to its high affinity receptor fc(ep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8y81 | ||||||
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Title | Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri | ||||||
Components |
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Keywords | IMMUNE SYSTEM / complex / antibody | ||||||
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 / FCERI mediated Ca+2 mobilization / Fc receptor mediated stimulatory signaling pathway / T cell differentiation involved in immune response / negative regulation of mast cell apoptotic process / high-affinity IgE receptor activity / IgE B cell receptor complex / type I hypersensitivity / Fc-gamma receptor III complex / mast cell apoptotic process / mast cell activation / FCERI mediated MAPK activation / serotonin secretion by platelet / positive regulation of interleukin-3 production / eosinophil degranulation / neutrophil activation involved in immune response / positive regulation of mast cell cytokine production / Fc-gamma receptor signaling pathway / positive regulation of mast cell degranulation / regulation of platelet activation / 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 / phagocytosis, engulfment / mast cell degranulation / 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 calcium-mediated signaling / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / SH2 domain binding / neutrophil chemotaxis / B cell differentiation / osteoclast differentiation / complement activation, classical pathway / establishment of localization in cell / protein localization to plasma membrane / integrin-mediated signaling pathway / calcium-mediated signaling / phosphoprotein binding / B cell receptor signaling pathway / receptor internalization / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / antibacterial humoral response / blood microparticle / 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 exosome / 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: 2.89 Å | ||||||
Authors | Du, S. / Deng, M.J. / Xiao, J.Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri Authors: Du, S. / Deng, M.J. / Xiao, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8y81.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8y81.ent.gz | 166.9 KB | Display | PDB format |
PDBx/mmJSON format | 8y81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8y81_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8y81_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8y81_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 8y81_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/8y81 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/8y81 | HTTPS FTP |
-Related structure data
Related structure data | 39029MC 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
-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 genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fcer1a, Fce1a / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P12371 |
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#2: Protein | Mass: 26747.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fce1b, Fcer1b / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P13386 |
#3: Protein | Mass: 13459.315 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fcer1g, Fce1g / Production host: Homo sapiens (human) / References: UniProt: P20411 |
-Protein / Non-polymers , 2 types, 3 molecules EF
#4: Protein | Mass: 41815.438 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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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.2 |
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: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 690272 / Symmetry type: POINT | ||||||||||||||||||||||||
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