|Entry||Database: EMDB / ID: 2073|
|Title||Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis|
|Keywords||Flavivirus / Dengue / NS1 / glycoprotein|
|Sample||Secreted form of DENV-2 NS1|
|Source||Dengue virus 2 / virus|
|Map data||3D reconstruction of recombinant DENV-2 sNS1 protein|
|Method||single particle reconstruction, at 23 Å resolution|
|Authors||Muller DA / Landsberg MJ / Bletchly C / Rothnagel R / Waddington L / Hankamer B / Young PR|
|Citation||J. Gen. Virol., 2012, 93, 771-779|
|Date||Deposition: Apr 13, 2012 / Header (metadata) release: Apr 17, 2012 / Map release: Apr 17, 2012 / Last update: Apr 17, 2012|
Downloads & links
|File||emd_2073.map.gz (map file in CCP4 format, 4922 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.86 Å|
CCP4 map header:
-Entire Secreted form of DENV-2 NS1
|Entire||Name: Secreted form of DENV-2 NS1 / Details: Monodisperse sample as assessed by SEC / Number of components: 1 / Oligomeric State: Homohexamer|
|Mass||Theoretical: 246 kDa|
-Component #1: protein, Non structural protein 1
|Protein||Name: Non structural protein 1 / a.k.a: NS1 / Oligomeric Details: Hexamer / Recombinant expression: Yes / Number of Copies: 6|
|Mass||Theoretical: 41 kDa|
|Source||Species: Dengue virus 2 / virus|
|Source (engineered)||Expression System: Spodoptera / arthropod / Vector: pFastBac|
|Source (natural)||Location in cell: Secreted|
|External references||InterPro: InterPro: 001157|
|Sample solution||Specimen conc.: 0.1 mg/ml / Buffer solution: 20 mM Tris, 300 mM NaCl / pH: 8|
|Support film||400 mesh copper grid with thin carbon support, glow discharged|
|Staining||Grids with adsorbed protein washed with an aqueous solution of 2% (w/v) uranyl acetate for 30 seconds.|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 12 / Date: Sep 17, 2003|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 68000 X (nominal)|
Astigmatism: objective lens astigmatism was corrected at 93,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 200 - 1000 nm
|Specimen Holder||Holder: FEI single tilt room temperature / Model: SIDE ENTRY, EUCENTRIC / Temperature: 295 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 40 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8|
|Processing||Method: single particle reconstruction / Number of class averages: 174 / Number of projections: 3523|
Details: Particles selected semi-automatically using the SWARM-PS software
Applied symmetry: C3 (3 fold cyclic)
|3D reconstruction||Algorithm: Angular reconstitution / Software: IMAGIC, EMAN, XMIPP|
Details: An exhaustive evaluation of point symmetry was performed as described in the associated manuscript
Resolution: 23 Å / Resolution method: FSC 0.5
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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
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