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- EMDB-3438: Three-dimensional reconstruction of W1118 strain Rosellinia necat... -

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Basic information

Entry
Database: EMDB / ID: 3438
TitleThree-dimensional reconstruction of W1118 strain Rosellinia necatrix quadrivirus 1
KeywordsdsRNA virus / quadrivirus / 3DR / fungal virus
SampleRosellinia necatrix quadrivirus 1 empty particles W1118 strain
SourceRosellinia necatrix quadrivirus 1 / virus / RnQV1
Map dataReconstruction of Rosellinia necatrix quadrivirus 1 strain W1075
Methodsingle particle (icosahedral) reconstruction, at 9.1 Å resolution
AuthorsLuque D / Mata CP / Gonzalez-Camacho F / Gonzalez JM / Gomez-Blanco J / Alfonso C / Rivas G / Havens WM / Kanematsu S / Suzuki N / Ghabrial SA / Trus BL / Caston JR
CitationJ. Virol., 2016, 90, 11220-11230

J. Virol., 2016, 90, 11220-11230 StrPapers
Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1.
Daniel Luque / Carlos P Mata / Fernando González-Camacho / José M González / Josué Gómez-Blanco / Carlos Alfonso / Germán Rivas / Wendy M Havens / Satoko Kanematsu / Nobuhiro Suzuki / Said A Ghabrial / Benes L Trus / José R Castón

DateDeposition: May 19, 2016 / Header (metadata) release: Aug 10, 2016 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3438.map.gz (map file in CCP4 format, 48779 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
232 pix
2.54 Å/pix.
= 589.28 Å
232 pix
2.54 Å/pix.
= 589.28 Å
232 pix
2.54 Å/pix.
= 589.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.54 Å
Density
Contour Level:0.6 (by author), 0.6 (movie #1):
Minimum - Maximum-0.91213852 - 1.70096147
Average (Standard dev.)0.01264894 (0.23093329)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions232232232
Origin000
Limit231231231
Spacing232232232
CellA=B=C: 589.27997 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z232232232
origin x/y/z0.0000.0000.000
length x/y/z589.280589.280589.280
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS232232232
D min/max/mean-0.9121.7010.013

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Supplemental data

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Sample components

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Entire Rosellinia necatrix quadrivirus 1 empty particles W1118 strain

EntireName: Rosellinia necatrix quadrivirus 1 empty particles W1118 strain
Number of components: 1 / Oligomeric State: icosahedral
MassTheoretical: 15.6 MDa / Experimental: 15.9 MDa / Measured by: Sedimentation

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Component #1: virus, Rosellinia necatrix quadrivirus 1

VirusName: Rosellinia necatrix quadrivirus 1 / a.k.a: RnQV1 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 15.6 MDa / Experimental: 15.9 MDa
SpeciesSpecies: Rosellinia necatrix quadrivirus 1 / virus / RnQV1 / Strain: W1118
Source (natural)Host Species: Rosellinia necatrix / Host category: FUNGI / Host species strain: W1118

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50 mM Tris-HCl pH 7.8, 5 mM EDTA, 150 mM NaCl
pH: 7.8
Support filmR 2/2 Quantifoil grids
StainingSamples were applied to grids, blotted and plunged into liquid ethane
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Feb 18, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3800 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 324 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 23926
3D reconstructionAlgorithm: Projection Matching / Software: Xmipp / CTF correction: Phase flipping & amplitude decay / Resolution: 9.1 Å / Resolution method: FSC 0.333, semi-independent

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