+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2062 | |||||||||
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Title | Cryphonectria nitschkei Virus (CnV)capsid | |||||||||
Map data | Reconstruction of Cryphonectria nitschkei Virus | |||||||||
Sample |
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Keywords | double-stranded RNA / fungal virus / viral structure / T=1 virus / duplicated helical fold | |||||||||
Biological species | Cryphonectria nitschkei chrysovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 8.1 Å | |||||||||
Authors | Gomez-Blanco J / Luque D / Gonzalez JM / Carrascosa JL / Alfonso C / Trus B / Havens WH / Ghabrial SA / Caston JR | |||||||||
Citation | Journal: J Virol / Year: 2012 Title: Cryphonectria nitschkei virus 1 structure shows that the capsid protein of chrysoviruses is a duplicated helix-rich fold conserved in fungal double-stranded RNA viruses. Authors: Josué Gómez-Blanco / Daniel Luque / José M González / José L Carrascosa / Carlos Alfonso / Benes Trus / Wendy M Havens / Said A Ghabrial / José R Castón / Abstract: Cryoelectron microscopy reconstruction of Cryphonectria nitschkei virus 1, a double-stranded RNA (dsRNA) virus, shows that the capsid protein (60 copies/particle) is formed by a repeated helical ...Cryoelectron microscopy reconstruction of Cryphonectria nitschkei virus 1, a double-stranded RNA (dsRNA) virus, shows that the capsid protein (60 copies/particle) is formed by a repeated helical core, indicative of gene duplication. This unusual organization is common to chrysoviruses. The arrangement of many of these putative α-helices is conserved in the totivirus L-A capsid protein, suggesting a shared motif. Our results indicate that a 120-subunit T=1 capsid is a conserved architecture that optimizes dsRNA replication and organization. | |||||||||
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_2062.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-2062-v30.xml emd-2062.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | EMD-2062.png emd_2062.png | 425.6 KB 425.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2062 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2062 | HTTPS FTP |
-Validation report
Summary document | emd_2062_validation.pdf.gz | 296.6 KB | Display | EMDB validaton report |
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Full document | emd_2062_full_validation.pdf.gz | 295.7 KB | Display | |
Data in XML | emd_2062_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2062 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2062 | 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_2062.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Cryphonectria nitschkei Virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.034 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 : Cryphonectria nitschkei virus
Entire | Name: Cryphonectria nitschkei virus |
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Components |
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-Supramolecule #1000: Cryphonectria nitschkei virus
Supramolecule | Name: Cryphonectria nitschkei virus / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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-Supramolecule #1: Cryphonectria nitschkei chrysovirus 1
Supramolecule | Name: Cryphonectria nitschkei chrysovirus 1 / type: virus / ID: 1 / Name.synonym: Cryphonectria nitschkei Virus / NCBI-ID: 399394 / Sci species name: Cryphonectria nitschkei chrysovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Cryphonectria nitschkei Virus |
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Host (natural) | Organism: Cryphonectria nitschkei (fungus) / synonym: FUNGI |
Molecular weight | Theoretical: 8.2 MDa |
Virus shell | Shell ID: 1 / Diameter: 400 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 / Details: 50 mM Tris-HCl pH 7.8, 5 mM EDTA,150 mM NaCl |
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Staining | Type: NEGATIVE Details: Samples were applied to grids, blotted and plunged into liquid ethane |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 98 K / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Dec 1, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 950 / Average electron dose: 10 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 62463 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Phase flipping & amplitude |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 18732 |