|Entry||Database: EMDB / ID: 5006|
|Title||Structure of immature Dengue virus at low pH|
|Keywords||Dengue virus / maturation|
|Sample||immature Dengue virus|
|Source||Dengue virus / virus / Dengue / デングウイルス|
|Map data||immature Dengue virus particle at pH 6|
|Method||single particle (icosahedral) reconstruction, at 25 Å resolution|
|Authors||Yu I / Zhang W / Holdaway HA / Li L / Kostyuchenko VA / Chipman PR / Kuhn RJ / Rossmann MG / Chen J|
|Citation||Science, 2008, 319, 1834-1837|
|Validation Report||PDB-ID: 3c6r|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 26, 2008 / Header (metadata) release: Mar 4, 2008 / Map release: Apr 22, 2009 / Last update: Feb 26, 2008|
Downloads & links
|File||emd_5006.map.gz (map file in CCP4 format, 64772 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.74 Å|
CCP4 map header:
-Entire immature Dengue virus
|Entire||Name: immature Dengue virus / Number of components: 1|
-Component #1: virus, Dengue virus
|Virus||Name: Dengue virus / a.k.a: Dengue / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN|
|Species||Species: Dengue virus / virus / Dengue / デングウイルス|
|Source (natural)||Host category: VERTEBRATES|
|Sample solution||Buffer solution: The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6|
|Support film||400 mesh copper grid|
|Vitrification||Instrument: NONE / Cryogen name: ETHANE|
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 51040 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2900 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 14 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1|
|Processing||Method: single particle (icosahedral) reconstruction / Number of projections: 231 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Fourier-Bessel Method / Euler angles: theta:69-90 degrees phi:(-31)-31 degrees / Software: EM3DR / CTF correction: each particle / Resolution: 25 Å / Resolution method: FSC 0.5|
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