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Yorodumi- EMDB-3351: Electron cryo-microscopy of an dsRNA-full Omono River virus (OmRV) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3351 | |||||||||
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Title | Electron cryo-microscopy of an dsRNA-full Omono River virus (OmRV) | |||||||||
Map data | Reconstruction of dsRNA-full OmRV | |||||||||
Sample |
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Keywords | Virus / totivirus / mosquito / totiviridae / double-stranded RNA / dsRNA / capsid / icosahedral / icosahedron / T=1 | |||||||||
Biological species | Omono River virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.9 Å | |||||||||
Authors | Okamoto K / Miyazaki N / Larsson DSD / Kobayashi D / Svenda M / Muehlig K / Maia FRNC / Gunn L-H / Isawa H / Kobayashi M ...Okamoto K / Miyazaki N / Larsson DSD / Kobayashi D / Svenda M / Muehlig K / Maia FRNC / Gunn L-H / Isawa H / Kobayashi M / Sawabe K / Murata K / Hajdu J | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes. Authors: Kenta Okamoto / Naoyuki Miyazaki / Daniel S D Larsson / Daisuke Kobayashi / Martin Svenda / Kerstin Mühlig / Filipe R N C Maia / Laura H Gunn / Haruhiko Isawa / Mutsuo Kobayashi / Kyoko ...Authors: Kenta Okamoto / Naoyuki Miyazaki / Daniel S D Larsson / Daisuke Kobayashi / Martin Svenda / Kerstin Mühlig / Filipe R N C Maia / Laura H Gunn / Haruhiko Isawa / Mutsuo Kobayashi / Kyoko Sawabe / Kazuyoshi Murata / Janos Hajdu / Abstract: Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper ...Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short "plug" structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts. | |||||||||
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_3351.map.gz | 78.1 MB | EMDB map data format | |
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Header (meta data) | emd-3351-v30.xml emd-3351.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | EMD3351-500pix.tif | 508.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3351 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3351 | HTTPS FTP |
-Validation report
Summary document | emd_3351_validation.pdf.gz | 253.9 KB | Display | EMDB validaton report |
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Full document | emd_3351_full_validation.pdf.gz | 253 KB | Display | |
Data in XML | emd_3351_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3351 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3351 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3351.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of dsRNA-full OmRV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.88 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 : dsRNA-full totivirus-like Omono River virus (OmRV)
Entire | Name: dsRNA-full totivirus-like Omono River virus (OmRV) |
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Components |
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-Supramolecule #1000: dsRNA-full totivirus-like Omono River virus (OmRV)
Supramolecule | Name: dsRNA-full totivirus-like Omono River virus (OmRV) / type: sample / ID: 1000 / Oligomeric state: T=1 (T=2) / Number unique components: 1 |
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-Supramolecule #1: Omono River virus
Supramolecule | Name: Omono River virus / type: virus / ID: 1 / Details: dsRNA-filled particle / NCBI-ID: 753758 / Sci species name: Omono River virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Culex mosquito / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 61 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 | 1.43 mg/mL |
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Buffer | pH: 7.5 / Details: 100 mM ammonium acetate |
Grid | Details: Holey carbon grid |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | JEOL 2200FS |
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Specialist optics | Energy filter - Name: Omega |
Date | Jan 13, 2016 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Liquid nitrogen cooled / Specimen holder model: JEOL |
-Image processing
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 6224 |
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