|Entry||Database: EMDB / ID: 2141|
|Title||6A Electron cryomicroscopy structure of immature Dengue virus serotype 1|
|Keywords||flavivirus / dengue virus serotype 1 / immature / e protein / prM protein / capsid protein|
|Sample||Immature Dengue virus serotype 1|
|Source||Dengue virus 1 / virus|
|Map data||immature Dengue virus 1|
|Method||single particle (icosahedral) reconstruction, at 6 Å resolution|
|Authors||Kostyuchenko VA / Zhang Q / Tan LC / Ng TS / Lok SM|
|Citation||J. Virol., 2013, 87, 7700-7707|
|Validation Report||PDB-ID: 4b03|
SummaryFull reportAbout validation report
|Date||Deposition: Jun 25, 2012 / Header (metadata) release: Jul 9, 2012 / Map release: Jun 5, 2013 / Last update: Jun 19, 2013|
Downloads & links
|File||emd_2141.map.gz (map file in CCP4 format, 843751 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.2 Å|
CCP4 map header:
-Entire Immature Dengue virus serotype 1
|Entire||Name: Immature Dengue virus serotype 1 / Number of components: 1|
|Mass||Theoretical: 14.5 MDa / Experimental: 14.5 MDa|
Measured by: estimation based on components' amino acid sequences
-Component #1: virus, Dengue virus 1
|Virus||Name: Dengue virus 1 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN|
|Mass||Theoretical: 14.5 MDa / Experimental: 14.5 MDa|
|Species||Species: Dengue virus 1 / virus / Strain: PVP159 (DEN1/SG/07K3640DK1/2008)|
|Source (natural)||Host Species: Aedes aegypti / arthropod / / Host category: INVERTEBRATES|
|Shell #1||Name of element: E / Diameter: 600 Å / T number(triangulation number): 1|
|Sample solution||pH: 7.5|
|Support film||thin carbon film on lacey carbon support, copper grid, plasma cleaned and glow discharged|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: blot 1 second before plunging|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Apr 11, 2012|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 17.7 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 75000 X (nominal), 75000 X (calibrated)|
Astigmatism: Astigmatism was corrected at 250,000 magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3500 nm / Energy filter: FEI
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 K ( 99 - 101 K)|
|Camera||Detector: GENERIC GATAN (4k x 4k)|
|Image acquisition||Number of digital images: 838 / Bit depth: 16 / Details: CCD data|
|Processing||Method: single particle (icosahedral) reconstruction / Number of projections: 7169 / Details: particles were manually selected / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: MPSA / Software: GPU-adapted, EMAN1|
CTF correction: Wiener filter weighting each particle during 3D reconstruction
Resolution: 6 Å / Resolution method: FSC 0.143
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