|Entry||Database: EMDB / ID: 5373|
|Title||Structural transitions in RCNMV revealing potential mechanism of RNA release (EDTA map)|
|Keywords||cryo-electron microscopy / virus / red clover necrotic mosaic virus|
|Source||Red clover necrotic mosaic virus / virus / RCNMV|
|Map data||this is EM map of native RCNMV with EDTA|
|Method||single particle (icosahedral) reconstruction, at 16.5 Å resolution|
|Authors||Sherman MB / Guenther RH / Tama F / Sit TL / Brooks CL / Mikhailov AM / Orlova EV / Baker TS / Lommel SA|
|Citation||J. Virol., 2006, 80, 10395-10406|
J. Virol., 2006, 80, 10395-10406 Yorodumi Papers
|Date||Deposition: Dec 16, 2011 / Header (metadata) release: Dec 19, 2011 / Map release: Dec 19, 2011 / Last update: Dec 19, 2011|
Downloads & links
|File||emd_5373.map.gz (map file in CCP4 format, 65537 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.97 Å|
CCP4 map header:
|Entire||Name: RCNMV / Details: monodisperse sample / Number of components: 1|
|Mass||Theoretical: 7 MDa|
-Component #1: virus, Red clover necrotic mosaic virus
|Virus||Name: Red clover necrotic mosaic virus / a.k.a: RCNMV / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES|
|Mass||Theoretical: 7 MDa / Experimental: 7 MDa|
|Species||Species: Red clover necrotic mosaic virus / virus / RCNMV|
|Source (natural)||Host Species: Dianthus / plant / Host category: PLANTAE(HIGHER PLANTS)|
|Sample solution||Specimen conc.: 1 mg/ml / Buffer solution: 10 mM Tris-HCl / pH: 6.5|
|Support film||200 mesh Quantifoil|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Details: Vitrification instrument: cryo-plunger|
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM300FEG/T / Date: Oct 15, 2003|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 47000 X (nominal), 49523 X (calibrated) / Astigmatism: manual / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2800 nm|
|Specimen Holder||Holder: GATAN 626 / Model: GATAN LIQUID NITROGEN / Temperature: 95 K ( 95 - 123 K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 1000 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 16 / OD range: 1.5|
|Processing||Method: single particle (icosahedral) reconstruction / Number of projections: 4000 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: PFT / Software: PFT / CTF correction: micrograph / Resolution: 16.5 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: SITUS / Refinement space: REAL / Details: Protocol: NNM|
Input PDB model: 2TBV
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