+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15857 | |||||||||
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Title | Rosellinia necatrix megabirnavirus 1-W779 empty capsid | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Rosellinia necatrix megabirnavirus 1/W779 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Wang H / Okamoto K / Miyazaki N / Suzuki N | |||||||||
Funding support | Sweden, Japan, 2 items
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Citation | Journal: PLoS Pathog / Year: 2023 Title: Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture. Authors: Han Wang / Lakha Salaipeth / Naoyuki Miyazaki / Nobuhiro Suzuki / Kenta Okamoto / Abstract: Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces ...Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Compared with other non-enveloped icosahedral dsRNA viruses, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15857.map.gz | 689.2 MB | EMDB map data format | |
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Header (meta data) | emd-15857-v30.xml emd-15857.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_15857.png | 259.5 KB | ||
Others | emd_15857_half_map_1.map.gz emd_15857_half_map_2.map.gz | 595.5 MB 595.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15857 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15857 | HTTPS FTP |
-Validation report
Summary document | emd_15857_validation.pdf.gz | 864.9 KB | Display | EMDB validaton report |
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Full document | emd_15857_full_validation.pdf.gz | 864.5 KB | Display | |
Data in XML | emd_15857_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_15857_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15857 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15857 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15857.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15857_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15857_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rosellinia necatrix megabirnavirus 1/W779
Entire | Name: Rosellinia necatrix megabirnavirus 1/W779 |
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Components |
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-Supramolecule #1: Rosellinia necatrix megabirnavirus 1/W779
Supramolecule | Name: Rosellinia necatrix megabirnavirus 1/W779 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 658904 / Sci species name: Rosellinia necatrix megabirnavirus 1/W779 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14602 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |