+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19895 | ||||||||||||
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Title | Structure of IgE HMM5 bound to FceRIa cryo-EM class 8 | ||||||||||||
Map data | map for class 8 of complex between IgE HMM5 and FceRIa ectodomain | ||||||||||||
Sample |
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Keywords | IgE / Fc receptor / allergy / antibody / IMMUNE SYSTEM | ||||||||||||
Function / homology | Function and homology information high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / type 2 immune response / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization ...high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / type 2 immune response / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | ||||||||||||
Authors | Andersen GR / Jensen RK | ||||||||||||
Funding support | Denmark, 3 items
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Citation | Journal: To be published Title: Structure of IgE HMM5 bound to FceRIa cryo-EM class 8 Authors: Andersen GR / Jensen RK | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19895.map.gz | 112.6 MB | EMDB map data format | |
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Header (meta data) | emd-19895-v30.xml emd-19895.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_19895.png | 88.9 KB | ||
Filedesc metadata | emd-19895.cif.gz | 6.1 KB | ||
Others | emd_19895_half_map_1.map.gz emd_19895_half_map_2.map.gz | 226.4 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19895 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19895 | HTTPS FTP |
-Validation report
Summary document | emd_19895_validation.pdf.gz | 1007.6 KB | Display | EMDB validaton report |
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Full document | emd_19895_full_validation.pdf.gz | 1007.1 KB | Display | |
Data in XML | emd_19895_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_19895_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19895 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19895 | HTTPS FTP |
-Related structure data
Related structure data | 9eq3MC 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_19895.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | map for class 8 of complex between IgE HMM5 and FceRIa ectodomain | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_19895_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_19895_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : complex of IgE HMM5 and the ectodomain of FceRIa
Entire | Name: complex of IgE HMM5 and the ectodomain of FceRIa |
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Components |
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-Supramolecule #1: complex of IgE HMM5 and the ectodomain of FceRIa
Supramolecule | Name: complex of IgE HMM5 and the ectodomain of FceRIa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 210 KDa |
-Macromolecule #1: IgE HMM5 heavy chain
Macromolecule | Name: IgE HMM5 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60.203508 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSLEESGGRL VTPGTPLTLT CTVSGFSLST YNIHWVRQAP GKGLEWIGVI DTGGGTYFAS WAKGRFAISK TSSTTVDLKM TSLTAADTA TYFCAKGFDY SASTNLWGPG TLVTISSAST QSPSVFPLTR CCKNIPSNAT SVTLGCLATG YFPEPVMVTW D TGSLNGTT ...String: QSLEESGGRL VTPGTPLTLT CTVSGFSLST YNIHWVRQAP GKGLEWIGVI DTGGGTYFAS WAKGRFAISK TSSTTVDLKM TSLTAADTA TYFCAKGFDY SASTNLWGPG TLVTISSAST QSPSVFPLTR CCKNIPSNAT SVTLGCLATG YFPEPVMVTW D TGSLNGTT MTLPATTLTL SGHYATISLL TVSGAWAKQM FTCRVAHTPS STDWVDNKTF SVCSRDFTPP TVKILQSSCD GG GHFPPTI QLLCLVSGYT PGTINITWLE DGQVMDVDLS TASTTQEGEL ASTQSELTLS QKHWLSDRTY TCQVTYQGHT FED STKKCA DSNPRGVSAY LSRPSPFDLF IRKSPTITCL VVDLAPSKGT VNLTWSRASG KPVNHSTRKE EKQRNGTLTV TSTL PVGTR DWIEGETYQC RVTHPHLPRA LMRSTTKTSG PRAAPEVYAF ATPEWPGSRD KRTLACLIQN FMPEDISVQW LHNEV QLPD ARHSTTQPRK TKGSGFFVFS RLEVTRAEWE QKDEFICRAV HEAASPSQTV QRAVSSVNPG KHHHHHH |
-Macromolecule #2: IgE HMM5 light chain
Macromolecule | Name: IgE HMM5 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.384795 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ELDMTQTPSS VSAPVGGSVT INCQSSQSVY GNNYLAWYQQ KAGQPPKLLI YRASTLASGA PSRFKGSGSG TQFTLTISDL ESDDAATYY CLGYYNGVIN VFGGGTNVEI KRTVGAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String: ELDMTQTPSS VSAPVGGSVT INCQSSQSVY GNNYLAWYQQ KAGQPPKLLI YRASTLASGA PSRFKGSGSG TQFTLTISDL ESDDAATYY CLGYYNGVIN VFGGGTNVEI KRTVGAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC |
-Macromolecule #3: High affinity immunoglobulin epsilon receptor subunit alpha
Macromolecule | Name: High affinity immunoglobulin epsilon receptor subunit alpha type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 19.88007 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KPKVSLNPPW NRIFKGENVT LTCNGNNFFE VSSTKWFHNG SLSEETNSSL NIVNAKFEDS GEYKCQHQQV NESEPVYLEV FSDWLLLQA SAEVVMEGQP LFLRCHGWRN WDVYKVIYYK DGEALKYWYE NHNISITNAT VEDSGTYYCT GKVWQLDYES E PLNITVIK APR UniProtKB: High affinity immunoglobulin epsilon receptor subunit alpha |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 8 / 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 | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.16 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19161 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |