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- EMDB-2062: Cryphonectria nitschkei Virus (CnV)capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2062
TitleCryphonectria nitschkei Virus (CnV)capsid
Map dataReconstruction of Cryphonectria nitschkei Virus
Sample
  • Sample: Cryphonectria nitschkei virus
  • Virus: Cryphonectria nitschkei chrysovirus 1
Keywordsdouble-stranded RNA / fungal virus / viral structure / T=1 virus / duplicated helical fold
Biological speciesCryphonectria nitschkei chrysovirus 1
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 8.1 Å
AuthorsGomez-Blanco J / Luque D / Gonzalez JM / Carrascosa JL / Alfonso C / Trus B / Havens WH / Ghabrial SA / Caston JR
CitationJournal: J Virol / Year: 2012
Title: Cryphonectria nitschkei virus 1 structure shows that the capsid protein of chrysoviruses is a duplicated helix-rich fold conserved in fungal double-stranded RNA viruses.
Authors: Josué Gómez-Blanco / Daniel Luque / José M González / José L Carrascosa / Carlos Alfonso / Benes Trus / Wendy M Havens / Said A Ghabrial / José R Castón /
Abstract: Cryoelectron microscopy reconstruction of Cryphonectria nitschkei virus 1, a double-stranded RNA (dsRNA) virus, shows that the capsid protein (60 copies/particle) is formed by a repeated helical ...Cryoelectron microscopy reconstruction of Cryphonectria nitschkei virus 1, a double-stranded RNA (dsRNA) virus, shows that the capsid protein (60 copies/particle) is formed by a repeated helical core, indicative of gene duplication. This unusual organization is common to chrysoviruses. The arrangement of many of these putative α-helices is conserved in the totivirus L-A capsid protein, suggesting a shared motif. Our results indicate that a 120-subunit T=1 capsid is a conserved architecture that optimizes dsRNA replication and organization.
History
DepositionMar 28, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateJan 22, 2014-
Current statusJan 22, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.425
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.425
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2062.png

emd_2062.png

Downloads & links

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Map

FileDownload / File: emd_2062.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Cryphonectria nitschkei Virus
Voxel sizeX=Y=Z: 2.034 Å
Density
Contour LevelBy AUTHOR: 0.425 / Movie #1: 0.425
Minimum - Maximum-0.62426001 - 1.48303425
Average (Standard dev.)0.01994015 (±0.17329407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 520.704 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0342.0342.034
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z520.704520.704520.704
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.6241.4830.020

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Supplemental data

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Sample components

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Entire : Cryphonectria nitschkei virus

EntireName: Cryphonectria nitschkei virus
Components
  • Sample: Cryphonectria nitschkei virus
  • Virus: Cryphonectria nitschkei chrysovirus 1

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Supramolecule #1000: Cryphonectria nitschkei virus

SupramoleculeName: Cryphonectria nitschkei virus / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1

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Supramolecule #1: Cryphonectria nitschkei chrysovirus 1

SupramoleculeName: Cryphonectria nitschkei chrysovirus 1 / type: virus / ID: 1 / Name.synonym: Cryphonectria nitschkei Virus / NCBI-ID: 399394 / Sci species name: Cryphonectria nitschkei chrysovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Cryphonectria nitschkei Virus
Host (natural)Organism: Cryphonectria nitschkei (fungus) / synonym: FUNGI
Molecular weightTheoretical: 8.2 MDa
Virus shellShell ID: 1 / Diameter: 400 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8 / Details: 50 mM Tris-HCl pH 7.8, 5 mM EDTA,150 mM NaCl
StainingType: NEGATIVE
Details: Samples were applied to grids, blotted and plunged into liquid ethane
VitrificationCryogen name: ETHANE / Chamber temperature: 98 K / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62463 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateDec 1, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 950 / Average electron dose: 10 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping & amplitude
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 18732

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