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Yorodumi- EMDB-1459: Partitivirus structure reveals a 120-subunit, helix-rich capsid w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1459 | |||||||||
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Title | Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers. | |||||||||
Map data | This is the final map calculated | |||||||||
Sample |
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Biological species | Penicillium stoloniferum virus S | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||
Authors | Ochoa WF / Havens WM / Sinkovits RS / Nibert ML / Ghabrial SA / Baker TS | |||||||||
Citation | Journal: Structure / Year: 2008 Title: Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers. Authors: Wendy F Ochoa / Wendy M Havens / Robert S Sinkovits / Max L Nibert / Said A Ghabrial / Timothy S Baker / Abstract: Two distinct partitiviruses, Penicillium stoloniferum viruses S and F, can be isolated from the fungus Penicillium stoloniferum. The bisegmented dsRNA genomes of these viruses are separately packaged ...Two distinct partitiviruses, Penicillium stoloniferum viruses S and F, can be isolated from the fungus Penicillium stoloniferum. The bisegmented dsRNA genomes of these viruses are separately packaged in icosahedral capsids containing 120 coat-protein subunits. We used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structure of Penicillium stoloniferum virus S at 7.3 A resolution. The capsid, approximately 350 A in outer diameter, contains 12 pentons, each of which is topped by five arched protrusions. Each of these protrusions is, in turn, formed by a quasisymmetric dimer of coat protein, for a total of 60 such dimers per particle. The density map shows numerous tubular features, characteristic of alpha helices and consistent with secondary structure predictions for the coat protein. This three-dimensional structure of a virus from the family Partitiviridae exhibits both similarities to and differences from the so-called "T = 2" capsids of other dsRNA viruses. | |||||||||
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_1459.map.gz | 38.7 MB | EMDB map data format | |
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Header (meta data) | emd-1459-v30.xml emd-1459.xml | 6.5 KB 6.5 KB | Display Display | EMDB header |
Images | 1459.gif | 36.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1459 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1459 | HTTPS FTP |
-Validation report
Summary document | emd_1459_validation.pdf.gz | 264.4 KB | Display | EMDB validaton report |
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Full document | emd_1459_full_validation.pdf.gz | 263.5 KB | Display | |
Data in XML | emd_1459_validation.xml.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1459 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1459 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1459.map.gz / Format: CCP4 / Size: 206 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the final map calculated | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 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 : PsV-S
Entire | Name: PsV-S |
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Components |
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-Supramolecule #1000: PsV-S
Supramolecule | Name: PsV-S / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Penicillium stoloniferum virus S
Supramolecule | Name: Penicillium stoloniferum virus S / type: virus / ID: 1 / Name.synonym: PsV-S / NCBI-ID: 216371 / Sci species name: Penicillium stoloniferum virus S / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: PsV-S |
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Host (natural) | Organism: Penicillium Stoloniferum (fungus) / synonym: FUNGI |
Virus shell | Shell ID: 1 / Name: PsV-S / Diameter: 35 Å / T number (triangulation number): 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE |
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-Electron microscopy
Microscope | FEI TECNAI SPHERA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: OTHER |
Sample stage | Specimen holder: Polara / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.5 CUT-OFF |
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