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- EMDB-3619: RnQV1-W1118 empty capsid -

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Basic information

Entry
Database: EMDB / ID: 3619
TitleRnQV1-W1118 empty capsid
SampleRosellinia necatrix quadrivirus 1
SourceRosellinia necatrix quadrivirus 1 / virus
Map dataRosellinia necatrix quadrivirus 1 strain W1118 (RnQV1-1118), empty particle
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsMata CP / Luque D / Gomez-Blanco J / Rodriguez JM / Suzuki N / Ghabrial SA / Carrascosa JL / Trus BL / Caston JR
CitationTo Be Published

To Be Published Search PubMed
Viral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus
Mata CP / Luque D / Gomez-Blanco J / Rodriguez JM / Suzuki N / Ghabrial SA / Carrascosa JL / Trus BL / Caston JR

Validation ReportPDB-ID: 5nd1

SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2017 / Header (metadata) release: Apr 19, 2017 / Map release: Nov 29, 2017 / Last update: Nov 29, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.18
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5nd1
  • Surface level: 0.18
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5nd1
  • Imaged by Jmol
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3619.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.18 (by author), 0.18 (movie #1):
Minimum - Maximum-0.852351 - 1.370603
Average (Standard dev.)0.0006925482 (0.09049471)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin-200-200-200
Limit199199199
Spacing400400400
CellA=B=C: 536 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.8521.3710.001

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Supplemental data

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Sample components

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Entire Rosellinia necatrix quadrivirus 1

EntireName: Rosellinia necatrix quadrivirus 1 / Number of components: 1
MassExperimental: 15.9 MDa

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Component #1: virus, Rosellinia necatrix quadrivirus 1

VirusName: Rosellinia necatrix quadrivirus 1 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassExperimental: 15.9 MDa
SpeciesSpecies: Rosellinia necatrix quadrivirus 1 / virus / Strain: W1118
Source (natural)Host Species: Rosellinia necatrix
Shell #1Name of element: P2 and P4 / Diameter: 470 Å / T number(triangulation number): 1

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50 mM Tris-HCl pH 7.8, 150 mM NaCl, 5 mM EDTA
pH: 7.8
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.7 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1125

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 37531
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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