+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0186 | |||||||||
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Title | Echovirus 18 Open particle without two pentamers | |||||||||
Map data | Echovirus 18 Open particle without two pentamers - C1 symmetry | |||||||||
Sample |
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Biological species | Echovirus E18 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.62 Å | |||||||||
Authors | Buchta D / Fuzik T / Hrebik D / Levdansky Y / Moravcova J / Plevka P | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Enterovirus particles expel capsid pentamers to enable genome release. Authors: David Buchta / Tibor Füzik / Dominik Hrebík / Yevgen Levdansky / Lukáš Sukeník / Liya Mukhamedova / Jana Moravcová / Robert Vácha / Pavel Plevka / Abstract: Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for ...Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for genome release. However, the mechanism of enterovirus uncoating is not well understood. Here, we use cryo-electron microscopy to visualize virions of human echovirus 18 in the process of genome release. We discover that the exit of the RNA from the particle of echovirus 18 results in a loss of one, two, or three adjacent capsid-protein pentamers. The opening in the capsid, which is more than 120 Å in diameter, enables the release of the genome without the need to unwind its putative double-stranded RNA segments. We also detect capsids lacking pentamers during genome release from echovirus 30. Thus, our findings uncover a mechanism of enterovirus genome release that could become target for antiviral drugs. | |||||||||
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_0186.map.gz | 89 MB | EMDB map data format | |
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Header (meta data) | emd-0186-v30.xml emd-0186.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0186_fsc.xml | 18.3 KB | Display | FSC data file |
Images | emd_0186.png | 248.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0186 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0186 | HTTPS FTP |
-Validation report
Summary document | emd_0186_validation.pdf.gz | 284.8 KB | Display | EMDB validaton report |
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Full document | emd_0186_full_validation.pdf.gz | 283.9 KB | Display | |
Data in XML | emd_0186_validation.xml.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0186 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0186 | HTTPS FTP |
-Related structure data
Related structure data | 0181C 0182C 0183C 0184C 0185C 0187C 0188C 0189C 0217C 6hbgC 6hbhC 6hbjC 6hbkC 6hblC 6hhtC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0186.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Echovirus 18 Open particle without two pentamers - C1 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Echovirus E18
Entire | Name: Echovirus E18 |
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Components |
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-Supramolecule #1: Echovirus E18
Supramolecule | Name: Echovirus E18 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 47506 / Sci species name: Echovirus E18 / Sci species strain: Metcalf / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 6.76 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 340.0 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||
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Buffer | pH: 6 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / 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 / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 6331 / Average exposure time: 1.0 sec. / Average electron dose: 45.2 e/Å2 Details: Images were collected in movie-mode at 39 frames per second |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.282 µm / Calibrated defocus min: 0.651 µm / Calibrated magnification: 79725 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 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 | Overall B value: 114.57 |
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