|Entry||Database: EMDB / ID: 1939|
|Title||Rabbit Hemorrhagic Disease Virus (RHDV)capsid calculated from merged wt, L17 and N42 data sets|
|Map data||RHDV Virus like particle capsid calculated from merged wt, L17 and L42 data sets|
|Sample||RHDV Virus Like Particle capsid calculated from merged wt, L17 and L42 data sets:|
|Keywords||cage design / molecular switch / protein engineering / structural polymorphism / virus assembly|
|Source||Rabbit hemorrhagic disease virus (VP1)|
|Method||single particle reconstruction / cryo EM / negative staining / 8.9 Å resolution|
|Authors||Luque D / Gonzalez JM / Gomez-Blanco J / Marabini R / Chichon J / Mena I / Angulo I / Carrascosa JL / Verdaguer N / Trus BL / Barcena J / Caston JR|
|Citation||Journal: J. Virol. / Year: 2012|
Title: Epitope insertion at the N-terminal molecular switch of the rabbit hemorrhagic disease virus T = 3 capsid protein leads to larger T = 4 capsids.
Authors: Daniel Luque / José M González / Josué Gómez-Blanco / Roberto Marabini / Javier Chichón / Ignacio Mena / Iván Angulo / José L Carrascosa / Nuria Verdaguer / Benes L Trus / Juan Bárcena / José R Castón
|Date||Deposition: Jul 19, 2011 / Header (metadata) release: Jul 29, 2011 / Map release: May 17, 2012 / Last update: Oct 10, 2012|
|Structure viewer||EM map: |
Downloads & links
|File||emd_1939.map.gz (map file in CCP4 format, 328235 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.4 Å|
CCP4 map header:
-Entire RHDV Virus Like Particle capsid calculated from merged wt, L17 an...
|Entire||Name: RHDV Virus Like Particle capsid calculated from merged wt, L17 and L42 data sets|
Number of components: 1 / Oligomeric State: Icosahedral virus
|Mass||Theoretical: 10.8 MDa|
-Component #1: virus, Rabbit hemorrhagic disease virus
|Virus||Name: Rabbit hemorrhagic disease virus / a.k.a: VP1 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 60 kDa|
|Species||Species: Rabbit hemorrhagic disease virus (VP1)|
|Source (natural)||Host Species: Oryctolagus cuniculus (rabbit) / Host category: VERTEBRATES|
|Specimen||Specimen state: particle / Method: negative staining, cryo EM|
|Sample solution||Buffer solution: 200 mM Na2PO4, 100 mM NaCl / pH: 6|
|Support film||R 2/2 Quantifoil grids|
|Staining||Samples were applied to grids, blotted and plunged into liquid ethane|
|Vitrification||Instrument: NONE / Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|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: 800 - 3000 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 229 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8|
|Processing||Method: single particle reconstruction / Number of projections: 23606 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Projection Matching / Software: Xmipp / CTF correction: Phase flipping & amplitude decay / Resolution: 8.9 Å / Resolution method: FSC 0.5|
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