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- EMDB-2073: Structure of the dengue virus glycoprotein non-structural protein... -

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Basic information

Entry
Database: EMDB / ID: 2073
TitleStructure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis
KeywordsFlavivirus / Dengue / NS1 / glycoprotein
SampleSecreted form of DENV-2 NS1
SourceDengue virus 2 / virus
Map data3D reconstruction of recombinant DENV-2 sNS1 protein
Methodsingle particle reconstruction, at 23 Å resolution
AuthorsMuller DA / Landsberg MJ / Bletchly C / Rothnagel R / Waddington L / Hankamer B / Young PR
CitationJ. Gen. Virol., 2012, 93, 771-779

J. Gen. Virol., 2012, 93, 771-779 StrPapers
Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis.
David A Muller / Michael J Landsberg / Cheryl Bletchly / Rosalba Rothnagel / Lynne Waddington / Ben Hankamer / Paul R Young

DateDeposition: Apr 13, 2012 / Header (metadata) release: Apr 17, 2012 / Map release: Apr 17, 2012 / Last update: Apr 13, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.04
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_2073.map.gz (map file in CCP4 format, 4922 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
108 pix
1.86 Å/pix.
= 200.88 Å
108 pix
1.86 Å/pix.
= 200.88 Å
108 pix
1.86 Å/pix.
= 200.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.86 Å
Density
Contour Level:1.04 (by author), 1.04 (movie #1):
Minimum - Maximum-3.1992631 - 6.28529167
Average (Standard dev.)0.02490416 (0.49955314)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions108108108
Origin-135-135-135
Limit-28-28-28
Spacing108108108
CellA=B=C: 200.88 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.861.861.86
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z200.880200.880200.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS-135-135-135
NC/NR/NS108108108
D min/max/mean-3.1996.2850.025

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Supplemental data

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Sample components

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Entire Secreted form of DENV-2 NS1

EntireName: Secreted form of DENV-2 NS1 / Details: Monodisperse sample as assessed by SEC / Number of components: 1 / Oligomeric State: Homohexamer
MassTheoretical: 246 kDa

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Component #1: protein, Non structural protein 1

ProteinName: Non structural protein 1 / a.k.a: NS1 / Oligomeric Details: Hexamer / Recombinant expression: Yes / Number of Copies: 6
MassTheoretical: 41 kDa
SourceSpecies: Dengue virus 2 / virus
Source (engineered)Expression System: Spodoptera / arthropod / Vector: pFastBac
Source (natural)Location in cell: Secreted
External referencesInterPro: InterPro: 001157

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 20 mM Tris, 300 mM NaCl / pH: 8
Support film400 mesh copper grid with thin carbon support, glow discharged
StainingGrids with adsorbed protein washed with an aqueous solution of 2% (w/v) uranyl acetate for 30 seconds.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Sep 17, 2003
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 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 HolderHolder: FEI single tilt room temperature / Model: SIDE ENTRY, EUCENTRIC / Temperature: 295 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 40 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8

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Image processing

ProcessingMethod: 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 reconstructionAlgorithm: 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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