+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39543 | |||||||||
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Title | Mouse Fc epsilon RI | |||||||||
Map data | Main map (B-factor sharpened) | |||||||||
Sample |
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Keywords | IgE / high-affinity IgE receptor / allergy / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information Platelet Adhesion to exposed collagen / IgE receptor activity / Fc-epsilon receptor I complex / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / negative regulation of mast cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / T cell differentiation involved in immune response ...Platelet Adhesion to exposed collagen / IgE receptor activity / Fc-epsilon receptor I complex / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / negative regulation of mast cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / T cell differentiation involved in immune response / high-affinity IgE receptor activity / GPVI-mediated activation cascade / FCERI mediated MAPK activation / mast cell apoptotic process / mast cell activation / Fc-gamma receptor III complex / FCERI mediated Ca+2 mobilization / positive regulation of interleukin-3 production / FCERI mediated NF-kB activation / serotonin secretion by platelet / positive regulation of mast cell cytokine production / Cell surface interactions at the vascular wall / 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 / 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 / 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 / Neutrophil degranulation / osteoclast differentiation / integrin-mediated signaling pathway / establishment of localization in cell / protein localization to plasma membrane / phosphoprotein binding / calcium-mediated signaling / receptor internalization / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of tumor necrosis factor production / positive regulation of immune response / cell surface receptor signaling pathway / endosome / defense response to bacterium / immune response / protein heterodimerization activity / membrane raft / external side of plasma membrane / innate immune response / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.87 Å | |||||||||
Authors | Zhang Z / Yui M / Ohto U / Shimizu T | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Mouse Fc epsilon RI Authors: Zhang Z / Yui M / Ohto U / Shimizu T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39543.map.gz | 97.1 MB | EMDB map data format | |
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Header (meta data) | emd-39543-v30.xml emd-39543.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
Images | emd_39543.png | 102.5 KB | ||
Filedesc metadata | emd-39543.cif.gz | 5.6 KB | ||
Others | emd_39543_additional_1.map.gz emd_39543_half_map_1.map.gz emd_39543_half_map_2.map.gz | 51 MB 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39543 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39543 | HTTPS FTP |
-Validation report
Summary document | emd_39543_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_39543_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_39543_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_39543_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39543 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39543 | HTTPS FTP |
-Related structure data
Related structure data | 8yrjMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_39543.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map (B-factor sharpened) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_39543_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39543_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39543_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mouse Fc epsilon RI
Entire | Name: Mouse Fc epsilon RI |
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Components |
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-Supramolecule #1: Mouse Fc epsilon RI
Supramolecule | Name: Mouse Fc epsilon RI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: High affinity immunoglobulin epsilon receptor subunit alpha
Macromolecule | Name: High affinity immunoglobulin epsilon receptor subunit alpha type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 31.646197 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MVTGRSAQLC LALLFMSLDV ILTATEKSVL TLDPPWIRIF TGEKVTLSCY GNNHLQMNST TKWIHNGTVS EVNSSHLVIV SATVQDSGK YICQKQGLFK SKPVYLNVTQ DWLLLQTSAD MVLVHGSFDI RCHGWKNWNV RKVIYYRNDH AFNYSYESPV S IREATLND ...String: MVTGRSAQLC LALLFMSLDV ILTATEKSVL TLDPPWIRIF TGEKVTLSCY GNNHLQMNST TKWIHNGTVS EVNSSHLVIV SATVQDSGK YICQKQGLFK SKPVYLNVTQ DWLLLQTSAD MVLVHGSFDI RCHGWKNWNV RKVIYYRNDH AFNYSYESPV S IREATLND SGTYHCKGYL RQVKYESDKF RIAVVKAYKC KYYWLQLIFP LLVAILFAVD TGLLLSTEEQ FKSVLEIQKT GK YKKVETE LLTENLYFQG DYKDDDDKHH HHHHHH UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha |
-Macromolecule #2: High affinity immunoglobulin epsilon receptor subunit gamma
Macromolecule | Name: High affinity immunoglobulin epsilon receptor subunit gamma type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 11.890856 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MISAVILFLL LLVEQAAALG EPQLCYILDA VLFLYGIVLT LLYCRLKIQV RKAAIASREK ADAVYTGLNT RSQETYETLK HEKPPQWSH PQFEKEQKLI SEEDL UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma |
-Macromolecule #3: High affinity immunoglobulin epsilon receptor subunit beta
Macromolecule | Name: High affinity immunoglobulin epsilon receptor subunit beta type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 27.166141 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDTENRSRAD LALPNPQESS SAPDIELLEA SPAKAAPPKQ TWRTFLKKEL EFLGATQILV GLICLCFGTI VCSVLYVSDF DEEVLLLYK LGYPFWGAVL FVLSGFLSII SERKNTLYLV RGSLGANIVS SIAAGTGIAM LILNLTNNFA YMNNCKNVTE D DGCFVASF ...String: MDTENRSRAD LALPNPQESS SAPDIELLEA SPAKAAPPKQ TWRTFLKKEL EFLGATQILV GLICLCFGTI VCSVLYVSDF DEEVLLLYK LGYPFWGAVL FVLSGFLSII SERKNTLYLV RGSLGANIVS SIAAGTGIAM LILNLTNNFA YMNNCKNVTE D DGCFVASF TTELVLMMLF LTILAFCSAV LFTIYRIGQE LESKKVPDDR LYEELNVYSP IYSELEDKGE TSSPVDSEQK LI SEEDL UniProtKB: High affinity immunoglobulin epsilon receptor subunit beta |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97368 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |