+Open data
-Basic information
Entry | Database: PDB / ID: 8y84 | ||||||
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Title | Structure of the high affinity receptor fc(epsilon)ri TM | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBDOY | ||||||
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 / 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 / cellular response to low-density lipoprotein particle stimulus / 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 / regulation of immune response / immunoglobulin mediated immune response / positive regulation of phagocytosis / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / SH2 domain binding / osteoclast differentiation / protein localization to plasma membrane / establishment of localization in cell / integrin-mediated signaling pathway / phosphoprotein binding / calcium-mediated signaling / receptor internalization / positive regulation of interleukin-6 production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / positive regulation of tumor necrosis factor production / endosome / cell surface receptor signaling pathway / defense response to bacterium / immune response / protein heterodimerization activity / 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 Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 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 high affinity receptor fc(epsilon)ri TM 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 | 8y84.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8y84.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 8y84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8y84_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8y84_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8y84_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 8y84_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/8y84 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/8y84 | HTTPS FTP |
-Related structure data
Related structure data | 39032MC 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: 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 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P20411 #4: Chemical | ChemComp-Y01 / | Has ligand of interest | 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
Component | Name: Structure of the high affinity receptor fc(epsilon)ri TM Type: COMPLEX / Entity ID: #1-#3 / 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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 698272 / Symmetry type: POINT | ||||||||||||||||||||||||
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