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- EMDB-60090: Structure of the ige-fc bound to its high affinity receptor fc(ep... -
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Open data
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Basic information
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Title | Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state3 | |||||||||
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![]() | Complex / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() 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 / 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 / B cell differentiation / osteoclast differentiation / protein localization to plasma membrane / establishment of localization in cell / integrin-mediated signaling pathway / phosphoprotein binding / B cell receptor signaling pathway / calcium-mediated signaling / receptor internalization / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of interleukin-6 production / peptide antigen binding / 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 / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / endosome / cell surface receptor signaling pathway / defense response to bacterium / immune response / protein heterodimerization activity / external side of plasma membrane / lysosomal 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
![]() | Du S / Deng MJ / Xiao JY | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structure of the ige-fc bound to its high affinity receptor fc(epsilon)ri state2 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 | ![]() | 118.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
Images | ![]() | 18.1 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 844.8 KB | Display | ![]() |
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Full document | ![]() | 844.3 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8zgtMC ![]() 8zgsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60090_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60090_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ige-fc bound to its high affinity receptor fc(epsilon)ri
Entire | Name: ige-fc bound to its high affinity receptor fc(epsilon)ri |
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Components |
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-Supramolecule #1: ige-fc bound to its high affinity receptor fc(epsilon)ri
Supramolecule | Name: ige-fc bound to its high affinity receptor fc(epsilon)ri type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: High affinity immunoglobulin epsilon receptor
Supramolecule | Name: High affinity immunoglobulin epsilon receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: IgE
Supramolecule | Name: IgE / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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-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: ![]() ![]() |
Molecular weight | Theoretical: 27.83016 KDa |
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: ![]() ![]() |
Molecular weight | Theoretical: 26.747752 KDa |
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: ![]() ![]() |
Molecular weight | Theoretical: 9.774509 KDa |
Sequence | String: MIPAVILFLL LLVEEAAALG EPQLCYILDA ILFLYGIVLT LLYCRLKIQV RKADIASREK SDAVYTGLNT RNQETYETLK HEKPPQ UniProtKB: High affinity immunoglobulin epsilon receptor subunit gamma |
-Macromolecule #4: Immunoglobulin heavy constant epsilon
Macromolecule | Name: Immunoglobulin heavy constant epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.155809 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSVPTQVLGL LLLWLTDARC DIARPVNITK PTVDLLHSSC DPNAFHSTIQ LYCFVYGHIQ NDVSIHWLMD DRKIYETHAQ NVLIKEEGK LASTYSRLNI TQQQWMSEST FTCKVTSQGE NYWAHTRRCS DDEPRGVITY LIPPSPLDLY ENGTPKLTCL V LDLESEEN ...String: MSVPTQVLGL LLLWLTDARC DIARPVNITK PTVDLLHSSC DPNAFHSTIQ LYCFVYGHIQ NDVSIHWLMD DRKIYETHAQ NVLIKEEGK LASTYSRLNI TQQQWMSEST FTCKVTSQGE NYWAHTRRCS DDEPRGVITY LIPPSPLDLY ENGTPKLTCL V LDLESEEN ITVTWVRERK KSIGSASQRS TKHHNATTSI TSILPVDAKD WIEGEGYQCR VDHPHFPKPI VRSITKAPGK RS APEVYVF LPPEEEEKDK RTLTCLIQNF FPEDISVQWL QDSKLIPKSQ HSTTTPLKYN GSNQRFFIFS RLEVTKALWT QTK QFTCRV IHEALREPRK LERTISKSLG NTSLRPSQAS MHHHHHHSRV DYKDDDDK UniProtKB: Immunoglobulin heavy constant epsilon |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 5 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #8: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 350802 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |