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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2062 | |||||||||
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Title | Cryphonectria nitschkei Virus (CnV)capsid | |||||||||
![]() | Reconstruction of Cryphonectria nitschkei Virus | |||||||||
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![]() | double-stranded RNA / fungal virus / viral structure / T=1 virus / duplicated helical fold | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 8.1 Å | |||||||||
![]() | Gomez-Blanco J / Luque D / Gonzalez JM / Carrascosa JL / Alfonso C / Trus B / Havens WH / Ghabrial SA / Caston JR | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.1 KB 9.1 KB | Display Display | ![]() |
Images | ![]() ![]() | 425.6 KB 425.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 296.6 KB | Display | ![]() |
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Full document | ![]() | 295.7 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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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 |