|Entry||Database: EMDB / ID: 3438|
|Title||Three-dimensional reconstruction of W1118 strain Rosellinia necatrix quadrivirus 1|
|Keywords||dsRNA virus / quadrivirus / 3DR / fungal virus|
|Sample||Rosellinia necatrix quadrivirus 1 empty particles W1118 strain|
|Source||Rosellinia necatrix quadrivirus 1 / virus / RnQV1|
|Map data||Reconstruction of Rosellinia necatrix quadrivirus 1 strain W1075|
|Method||single particle (icosahedral) reconstruction, at 9.1 Å resolution|
|Authors||Luque D / Mata CP / Gonzalez-Camacho F / Gonzalez JM / Gomez-Blanco J / Alfonso C / Rivas G / Havens WM / Kanematsu S / Suzuki N / Ghabrial SA / Trus BL / Caston JR|
|Citation||J. Virol., 2016, 90, 11220-11230|
J. Virol., 2016, 90, 11220-11230 Yorodumi Papers
|Date||Deposition: May 19, 2016 / Header (metadata) release: Aug 10, 2016 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017|
Downloads & links
|File||emd_3438.map.gz (map file in CCP4 format, 48779 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.54 Å|
CCP4 map header:
-Entire Rosellinia necatrix quadrivirus 1 empty particles W1118 strain
|Entire||Name: Rosellinia necatrix quadrivirus 1 empty particles W1118 strain|
Number of components: 1 / Oligomeric State: icosahedral
|Mass||Theoretical: 15.6 MDa / Experimental: 15.9 MDa / Measured by: Sedimentation|
-Component #1: virus, Rosellinia necatrix quadrivirus 1
|Virus||Name: Rosellinia necatrix quadrivirus 1 / a.k.a: RnQV1 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 15.6 MDa / Experimental: 15.9 MDa|
|Species||Species: Rosellinia necatrix quadrivirus 1 / virus / RnQV1 / Strain: W1118|
|Source (natural)||Host Species: Rosellinia necatrix / Host category: FUNGI / Host species strain: W1118|
|Sample solution||Buffer solution: 50 mM Tris-HCl pH 7.8, 5 mM EDTA, 150 mM NaCl|
|Support film||R 2/2 Quantifoil grids|
|Staining||Samples were applied to grids, blotted and plunged into liquid ethane|
|Vitrification||Instrument: LEICA EM CPC / Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Feb 18, 2014|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 50000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3800 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 324 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8|
|Processing||Method: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 23926|
|3D reconstruction||Algorithm: Projection Matching / Software: Xmipp / CTF correction: Phase flipping & amplitude decay / Resolution: 9.1 Å / Resolution method: FSC 0.333, semi-independent|
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