+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0183 | |||||||||
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Title | Echovirus 18 empty particle | |||||||||
Map data | Echovirus 18 empty particle | |||||||||
Sample |
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Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Echovirus E18 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Buchta D / Fuzik T / Hrebik D / Levdansky Y / Moravcova J / Plevka P | |||||||||
Funding support | Czech Republic, 1 items
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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_0183.map.gz | 52.8 MB | EMDB map data format | |
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Header (meta data) | emd-0183-v30.xml emd-0183.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0183_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_0183.png | 351 KB | ||
Others | emd_0183_half_map_1.map.gz emd_0183_half_map_2.map.gz | 406.5 MB 405.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0183 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0183 | HTTPS FTP |
-Validation report
Summary document | emd_0183_validation.pdf.gz | 478.7 KB | Display | EMDB validaton report |
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Full document | emd_0183_full_validation.pdf.gz | 477.8 KB | Display | |
Data in XML | emd_0183_validation.xml.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0183 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0183 | HTTPS FTP |
-Related structure data
Related structure data | 6hbjMC 0181C 0182C 0184C 0185C 0186C 0187C 0188C 0189C 0217C 6hbgC 6hbhC 6hbkC 6hblC 6hhtC 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_0183.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Echovirus 18 empty particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Echovirus 18 empty particle half-map
File | emd_0183_half_map_1.map | ||||||||||||
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Annotation | Echovirus 18 empty particle half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Echovirus 18 empty particle half-map
File | emd_0183_half_map_2.map | ||||||||||||
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Annotation | Echovirus 18 empty particle half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: all / NCBI-ID: 47506 / Sci species name: Echovirus E18 / Sci species strain: Metcalf / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 5.24 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 330.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Viral protein 1
Macromolecule | Name: Viral protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Echovirus E18 |
Molecular weight | Theoretical: 32.564445 KDa |
Sequence | String: GDNQDRTVAN TQPSGPSNST EIPALTAVET GHTSQVDPSD TIQTRHVVNF HSRSESTIEN FMGRAACVFM DQYKINGEET STDRFAVWT INIREMAQLR RKCEMFTYMR FDIEMTMVIT SCQDQGTILD QDMPVLTHQI MYVPPGGPIP AKVDGYEWQT S TNPSVFWT ...String: GDNQDRTVAN TQPSGPSNST EIPALTAVET GHTSQVDPSD TIQTRHVVNF HSRSESTIEN FMGRAACVFM DQYKINGEET STDRFAVWT INIREMAQLR RKCEMFTYMR FDIEMTMVIT SCQDQGTILD QDMPVLTHQI MYVPPGGPIP AKVDGYEWQT S TNPSVFWT EGNAPPRISI PFISVGNAYS SFYDGWSHFT QDGTYGYTTL NAMGKLYIRH VNRSSPHQIT STIRVYFKPK HI KAWVPRP PRLCPYINKR DVNFVVTEIT DSRTSITDTP HPEHSVLATH |
-Macromolecule #2: Viral protein 2
Macromolecule | Name: Viral protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Echovirus E18 |
Molecular weight | Theoretical: 28.802328 KDa |
Sequence | String: SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDREATAE DQPTQPDVAT CRFYTLESVQ WEKTSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTDT TFPATELTTE DTPHVFTSDS I TGKKVQAA ...String: SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDREATAE DQPTQPDVAT CRFYTLESVQ WEKTSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTDT TFPATELTTE DTPHVFTSDS I TGKKVQAA VCNAGMGVGV GNLTIFPHQW INLRTNNSAT IVIPYINSVP MDNMFRHYNF TLMIIPFAPL NFTDGATAYV PI TVTIAPM YAEYNGLRLA STQ |
-Macromolecule #3: Viral protein 3
Macromolecule | Name: Viral protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Echovirus E18 |
Molecular weight | Theoretical: 26.143783 KDa |
Sequence | String: GVPVLNTPGS NQFLTSDDYQ SPSAMPQFDE TPEMHIPGEV RNLMEIAEVD SVVPVNNVTG KTKSMDAYQI PVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPTSRKDA MLGTHIVWDI G LQSSCVLC ...String: GVPVLNTPGS NQFLTSDDYQ SPSAMPQFDE TPEMHIPGEV RNLMEIAEVD SVVPVNNVTG KTKSMDAYQI PVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPTSRKDA MLGTHIVWDI G LQSSCVLC VPWISQSHYR MVQQDPYTSA GYITCWYQTN IVVPPGAPTS CDVLCFASAC NDFSVRLLRD TPFMAQPGKL Q |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.0 mg/mL | |||||||||||||||
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Buffer | pH: 5.8 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 II (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: 3 / Number real images: 16784 / Average exposure time: 1.0 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.816 µm / Calibrated defocus min: 0.357 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
Details | Reciprocal space refinement of atom positions and group B-factors |
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Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 117.89 / Target criteria: R-factors |
Output model | PDB-6hbj: |