+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39032 | |||||||||
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Title | Structure of the high affinity receptor fc(epsilon)ri TM | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ANTIBDOY / IMMUNE SYSTEM | |||||||||
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 / 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 / SH2 domain binding / neutrophil chemotaxis / osteoclast differentiation / establishment of localization in cell / protein localization to plasma membrane / integrin-mediated signaling pathway / calcium-mediated signaling / phosphoprotein binding / receptor internalization / 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 / cell surface receptor signaling pathway / endosome / 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 | single particle reconstruction / cryo EM / Resolution: 2.98 Å | |||||||||
Authors | Du S / Deng MJ / Xiao JY | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Structure of the high affinity receptor fc(epsilon)ri TM Authors: Du S / Deng MJ / Xiao JY | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39032.map.gz | 79.1 MB | EMDB map data format | |
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Header (meta data) | emd-39032-v30.xml emd-39032.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_39032.png | 25.9 KB | ||
Filedesc metadata | emd-39032.cif.gz | 5.3 KB | ||
Others | emd_39032_half_map_1.map.gz emd_39032_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39032 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39032 | HTTPS FTP |
-Validation report
Summary document | emd_39032_validation.pdf.gz | 724.8 KB | Display | EMDB validaton report |
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Full document | emd_39032_full_validation.pdf.gz | 724.4 KB | Display | |
Data in XML | emd_39032_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_39032_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39032 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39032 | HTTPS FTP |
-Related structure data
Related structure data | 8y84MC 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_39032.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_39032_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39032_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of the high affinity receptor fc(epsilon)ri TM
Entire | Name: Structure of the high affinity receptor fc(epsilon)ri TM |
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Components |
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-Supramolecule #1: Structure of the high affinity receptor fc(epsilon)ri TM
Supramolecule | Name: Structure of the high affinity receptor fc(epsilon)ri TM type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-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: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 27.83016 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDTGGSARLC LALVLISLGV MLTATQKSVV SLDPPWIRIL TGDKVTLICN GNNSSQMNST KWIHNDSISN VKSSHWVIVS ATIQDSGKY ICQKQGFYKS KPVYLNVMQE WLLLQSSADV VLDNGSFDIR CRSWKKWKVH KVIYYKDDIA FKYSYDSNNI S IRKATFND ...String: MDTGGSARLC LALVLISLGV MLTATQKSVV SLDPPWIRIL TGDKVTLICN GNNSSQMNST KWIHNDSISN VKSSHWVIVS ATIQDSGKY ICQKQGFYKS KPVYLNVMQE WLLLQSSADV VLDNGSFDIR CRSWKKWKVH KVIYYKDDIA FKYSYDSNNI S IRKATFND SGSYHCTGYL NKVECKSDKF SIAVVKDYTI EYRWLQLIFP SLAVILFAVD TGLWFSTHKQ FESILKIQKT GK GKKKG UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha |
-Macromolecule #2: High affinity immunoglobulin epsilon receptor subunit beta
Macromolecule | Name: High affinity immunoglobulin epsilon receptor subunit beta type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 26.747752 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDTENKSRAD LALPNPQESP SAPDIELLEA SPPAKALPEK PASPPPQQTW QSFLKKELEF LGVTQVLVGL ICLCFGTVVC STLQTSDFD DEVLLLYRAG YPFWGAVLFV LSGFLSIMSE RKNTLYLVRG SLGANIVSSI AAGLGIAILI LNLSNNSAYM N YCKDITED ...String: MDTENKSRAD LALPNPQESP SAPDIELLEA SPPAKALPEK PASPPPQQTW QSFLKKELEF LGVTQVLVGL ICLCFGTVVC STLQTSDFD DEVLLLYRAG YPFWGAVLFV LSGFLSIMSE RKNTLYLVRG SLGANIVSSI AAGLGIAILI LNLSNNSAYM N YCKDITED DGCFVTSFIT ELVLMLLFLT ILAFCSAVLL IIYRIGQEFE RSKVPDDRLY EELHVYSPIY SALEDTREAS AP VVS UniProtKB: High affinity immunoglobulin epsilon receptor subunit beta |
-Macromolecule #3: High affinity immunoglobulin epsilon receptor subunit gamma
Macromolecule | Name: High affinity immunoglobulin epsilon receptor subunit gamma type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 13.459315 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MIPAVILFLL LLVEEAAALG EPQLCYILDA ILFLYGIVLT LLYCRLKIQV RKADIASREK SDAVYTGLNT RNQETYETLK HEKPPQGSG WSHPQFEKGS GDYKDDDDKG SGWSHPQFEK UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma |
-Macromolecule #4: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 698272 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |