+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16378 | ||||||||||||
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Title | Structure of IgE bound to the ectodomain of FceRIa | ||||||||||||
Map data | consensus map | ||||||||||||
Sample |
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Function / homology | Function and homology information high-affinity IgE receptor activity / adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / IgD immunoglobulin complex / eosinophil degranulation / IgM immunoglobulin complex ...high-affinity IgE receptor activity / adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / IgD immunoglobulin complex / eosinophil degranulation / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / macrophage activation / IgE binding / type 2 immune response / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / mast cell degranulation / B cell proliferation / macrophage differentiation / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Potential therapeutics for SARS / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / cell surface receptor signaling pathway / inflammatory response / immune response / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Andersen GR / Jensen RK | ||||||||||||
Funding support | Denmark, 3 items
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Citation | Journal: To Be Published Title: Structure of IgE bound to the ectodomain of FceRIa 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_16378.map.gz | 120.3 MB | EMDB map data format | |
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Header (meta data) | emd-16378-v30.xml emd-16378.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_16378.png | 84.2 KB | ||
Others | emd_16378_half_map_1.map.gz emd_16378_half_map_2.map.gz | 222.6 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16378 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16378 | HTTPS FTP |
-Validation report
Summary document | emd_16378_validation.pdf.gz | 595.6 KB | Display | EMDB validaton report |
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Full document | emd_16378_full_validation.pdf.gz | 595.2 KB | Display | |
Data in XML | emd_16378_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_16378_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16378 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16378 | HTTPS FTP |
-Related structure data
Related structure data | 8c1cMC 8c1bC 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_16378.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | consensus map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.03625 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B for consensus map
File | emd_16378_half_map_1.map | ||||||||||||
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Annotation | half map B for consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A for consensus map
File | emd_16378_half_map_2.map | ||||||||||||
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Annotation | half map A for consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : IgE-FceRIa complex
Entire | Name: IgE-FceRIa complex |
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Components |
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-Supramolecule #1: IgE-FceRIa complex
Supramolecule | Name: IgE-FceRIa complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 Details: complex of IgE bound to the ectodomain of the FceRIa subunit |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: Immunoglobulin heavy constant epsilon
Macromolecule | Name: Immunoglobulin heavy constant epsilon / 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: 46.831613 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ASTQSPSVFP LTRCCKNIPS NATSVTLGCL ATGYFPEPVM VTWDTGSLNG TTMTLPATTL TLSGHYATIS LLTVSGAWAK QMFTCRVAH TPSSTDWVDN KTFSVCSRDF TPPTVKILQS SCDGGGHFPP TIQLLCLVSG YTPGTINITW LEDGQVMDVD L STASTTQE ...String: ASTQSPSVFP LTRCCKNIPS NATSVTLGCL ATGYFPEPVM VTWDTGSLNG TTMTLPATTL TLSGHYATIS LLTVSGAWAK QMFTCRVAH TPSSTDWVDN KTFSVCSRDF TPPTVKILQS SCDGGGHFPP TIQLLCLVSG YTPGTINITW LEDGQVMDVD L STASTTQE GELASTQSEL TLSQKHWLSD RTYTCQVTYQ GHTFEDSTKK CADSNPRGVS AYLSRPSPFD LFIRKSPTIT CL VVDLAPS KGTVNLTWSR ASGKPVNHST RKEEKQRNGT LTVTSTLPVG TRDWIEGETY QCRVTHPHLP RALMRSTTKT SGP RAAPEV YAFATPEWPG SRDKRTLACL IQNFMPEDIS VQWLHNEVQL PDARHSTTQP RKTKGSGFFV FSRLEVTRAE WEQK DEFIC RAVHEAASPS QTVQRAVSSV A |
-Macromolecule #2: Immunoglobulin kappa constant
Macromolecule | Name: Immunoglobulin kappa constant / 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: 11.763983 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: RTVGAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEV THQGLSSPVT KSFNRGEC |
-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 |
-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: 2 / 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
Concentration | 3.1 mg/mL |
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Buffer | pH: 7.5 |
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 / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / In silico model: Stochastic gradient descent based model |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 573328 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |