|Entry||Database: EMDB / ID: 5184|
|Title||The structure of JC polyomavirus treated with 250 mM L-arginine (pH 10.7)|
|Keywords||JC / JCV / polyomavirus / arginine|
|Sample||JC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)|
|Source||JC polyomavirus / virus / JCV|
|Map data||Cryo-EM based reconstruction of JC polyomavirus treated with 250 mM L-arginine|
|Method||single particle (icosahedral) reconstruction, at 17.6 Å resolution|
|Authors||Shen PS / Enderlein D / Nelson C / Carter WS / Kawano M / Xing L / Swenson RD / Olson NH / Baker TS / Cheng RH / Atwood WJ / Johne R / Belnap DM|
|Citation||Virology, 2011, 411, 142-152|
Virology, 2011, 411, 142-152 Yorodumi Papers
|Date||Deposition: Apr 12, 2010 / Header (metadata) release: Dec 8, 2010 / Map release: Jan 19, 2011 / Last update: Sep 23, 2011|
Downloads & links
|File||emd_5184.map.gz (map file in CCP4 format, 193091 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.59 Å|
CCP4 map header:
-Entire JC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)
|Entire||Name: JC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)|
Number of components: 1 / Oligomeric State: virions
-Component #1: virus, JC polyomavirus
|Virus||Name: JC polyomavirus / a.k.a: JCV / Class: VIRION / Details: Cryo-EM of JC polyomavirus over holey carbon grids / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: JC polyomavirus / virus / JCV|
|Source (natural)||Host Species: Homo sapiens / human / Host category: VERTEBRATES|
|Shell #1||Name of element: VP1 / Diameter: 5000 Å / T number(triangulation number): 7|
|Sample solution||Specimen conc.: 1.5 mg/ml|
Buffer solution: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2, 250 mM L-arginine
|Support film||200 mesh copper grid (holey carbon)|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: 3 second blot before plunging|
Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: Apr 23, 2007|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 39000 X (nominal), 39000 X (calibrated)|
Astigmatism: astigmatism was corrected at 59,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 4900 nm
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 88 - 95 K)
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 50 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16 / Details: Micrographs digitized in positive contrast mode.|
|Processing||Method: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: common lines / Software: PFT2 and EM3DR2 / CTF correction: each micrograph / Resolution: 17.6 Å / Resolution method: FSC 0.333|
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