+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12028 | |||||||||
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Title | Structure of echovirus 18 in complex with neonatal Fc receptor | |||||||||
Map data | The complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin | |||||||||
Sample |
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Keywords | complex / echovirus 18 virion / neonatal fc receptor / fcrn / beta-2-microglobulin / microglobulin / pocket factor / VIRUS | |||||||||
Function / homology | Function and homology information IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / T=pseudo3 icosahedral viral capsid / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / host cell cytoplasmic vesicle membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / cytoplasmic vesicle membrane / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / endocytosis involved in viral entry into host cell / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / nucleoside-triphosphate phosphatase / DAP12 signaling / MHC class II protein complex binding / protein complex oligomerization / early endosome membrane / late endosome membrane / monoatomic ion channel activity / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / DNA replication / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / RNA helicase activity / endosome membrane / induction by virus of host autophagy / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / proteolysis Similarity search - Function | |||||||||
Biological species | Echovirus E18 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Buchta D / Levdansky Y | |||||||||
Funding support | Czech Republic, 1 items
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Citation | Journal: To Be Published Title: Structure of echovirus 18 in complex with neonatal Fc receptor Authors: Buchta D / Levdansky Y / Fuzik T / Mukhamedova L / Moravcova J / Hrebik D / Andersen JT / Plevka P | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12028.map.gz | 76.2 MB | EMDB map data format | |
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Header (meta data) | emd-12028-v30.xml emd-12028.xml | 25.7 KB 25.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12028_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_12028.png | 266.3 KB | ||
Filedesc metadata | emd-12028.cif.gz | 7.3 KB | ||
Others | emd_12028_half_map_1.map.gz emd_12028_half_map_2.map.gz | 409.9 MB 409.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12028 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12028 | HTTPS FTP |
-Validation report
Summary document | emd_12028_validation.pdf.gz | 992.5 KB | Display | EMDB validaton report |
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Full document | emd_12028_full_validation.pdf.gz | 992.1 KB | Display | |
Data in XML | emd_12028_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_12028_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12028 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12028 | HTTPS FTP |
-Related structure data
Related structure data | 7b5fMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12028.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.061 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: The complex of echovirus 18 virion with heterodimer...
File | emd_12028_half_map_1.map | ||||||||||||
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Annotation | The complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: The complex of echovirus 18 virion with heterodimer...
File | emd_12028_half_map_2.map | ||||||||||||
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Annotation | The complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of echovirus 18 in complex with neonatal Fc receptor
+Supramolecule #1: Structure of echovirus 18 in complex with neonatal Fc receptor
+Supramolecule #2: Echovirus 18 native virion
+Supramolecule #3: Heterodimer of neonatal Fc Receptor and beta-2-microglobulin
+Macromolecule #1: Echovirus 18 viral protein 3
+Macromolecule #2: Echovirus 18 viral protein 4
+Macromolecule #3: Echovirus 18 viral protein 1
+Macromolecule #4: Echovirus 18 viral protein 2
+Macromolecule #5: IgG receptor FcRn large subunit p51
+Macromolecule #6: Beta-2-microglobulin
+Macromolecule #7: PALMITIC ACID
+Macromolecule #8: GUANINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.00 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.3 Component:
Details: Mixed in 1:1 volume ratio {20 mM Tris (pH=7.2), 100 mM NaCl} and {8 mM Na2HPO4, 2 mM KH2PO4 (pH=7.4), 137 mM NaCl, 2.7 mM KCl}=PBS | ||||||||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 4531 / Average exposure time: 1.27 sec. / Average electron dose: 54.48 e/Å2 / Details: Images were collected in movie-mode at 50 frames. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 75000 |
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
-Atomic model buiding 1
Refinement | Target criteria: R-factors |
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Output model | PDB-7b5f: |