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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0186 | |||||||||
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Title | Echovirus 18 Open particle without two pentamers | |||||||||
![]() | Echovirus 18 Open particle without two pentamers - C1 symmetry | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.62 Å | |||||||||
![]() | Buchta D / Fuzik T / Hrebik D / Levdansky Y / Moravcova J / Plevka P | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 89 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.3 KB | Display | ![]() |
Images | ![]() | 248.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 284.8 KB | Display | ![]() |
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Full document | ![]() | 283.9 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Echovirus 18 Open particle without two pentamers - C1 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Echovirus E18
Entire | Name: ![]() |
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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: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Overall B value: 114.57 |
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