+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5412 | |||||||||
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Title | CryoEM icosahedral reconstruction of AHSV7 | |||||||||
Map data | AHSV7 truncated VP2 filled | |||||||||
Sample |
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Keywords | AHSV7 | |||||||||
Biological species | African horse sickness virus 7 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.4 Å | |||||||||
Authors | Manole V / Laurinmaki P / Wyngaardt WV / Potgieter CA / Wright IM / Venter GJ / Dijk AAV / Sewell BT / Butcher SJ | |||||||||
Citation | Journal: J Virol / Year: 2012 Title: Structural insight into African horsesickness virus infection. Authors: Violeta Manole / Pasi Laurinmäki / Wouter Van Wyngaardt / Christiaan A Potgieter / Isabella M Wright / Gert J Venter / Alberdina A van Dijk / B Trevor Sewell / Sarah J Butcher / Abstract: African horsesickness (AHS) is a devastating disease of horses. The disease is caused by the double-stranded RNA-containing African horsesickness virus (AHSV). Using electron cryomicroscopy and three- ...African horsesickness (AHS) is a devastating disease of horses. The disease is caused by the double-stranded RNA-containing African horsesickness virus (AHSV). Using electron cryomicroscopy and three-dimensional image reconstruction, we determined the architecture of an AHSV serotype 4 (AHSV-4) reference strain. The structure revealed triple-layered AHS virions enclosing the segmented genome and transcriptase complex. The innermost protein layer contains 120 copies of VP3, with the viral polymerase, capping enzyme, and helicase attached to the inner surface of the VP3 layer on the 5-fold axis, surrounded by double-stranded RNA. VP7 trimers form a second, T=13 layer on top of VP3. Comparative analyses of the structures of bluetongue virus and AHSV-4 confirmed that VP5 trimers form globular domains and VP2 trimers form triskelions, on the virion surface. We also identified an AHSV-7 strain with a truncated VP2 protein (AHSV-7 tVP2) which outgrows AHSV-4 in culture. Comparison of AHSV-7 tVP2 to bluetongue virus and AHSV-4 allowed mapping of two domains in AHSV-4 VP2, and one in bluetongue virus VP2, that are important in infection. We also revealed a protein plugging the 5-fold vertices in AHSV-4. These results shed light on virus-host interactions in an economically important orbivirus to help the informed design of new vaccines. | |||||||||
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_5412.map.gz | 129.1 MB | EMDB map data format | |
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Header (meta data) | emd-5412-v30.xml emd-5412.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_5412_1.jpg | 191.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5412 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5412 | HTTPS FTP |
-Validation report
Summary document | emd_5412_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_5412_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_5412_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5412 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5412 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5412.map.gz / Format: CCP4 / Size: 251.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AHSV7 truncated VP2 filled | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8 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 : AHSV7 truncated VP2 filled
Entire | Name: AHSV7 truncated VP2 filled |
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Components |
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-Supramolecule #1000: AHSV7 truncated VP2 filled
Supramolecule | Name: AHSV7 truncated VP2 filled / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: African horse sickness virus 7
Supramolecule | Name: African horse sickness virus 7 / type: virus / ID: 1 / Name.synonym: AHSV7 / NCBI-ID: 86061 / Sci species name: African horse sickness virus 7 / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: AHSV7 |
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Host (natural) | Organism: Equus caballus (horse) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Name: VP2 and VP5 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.5 / Details: 2mM Tris-HCl |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Feb 1, 2010 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Number real images: 507 / Average electron dose: 18 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 83000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 83000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 2798 |