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- EMDB-3437: Three-dimensional reconstruction of W1075 strain Rosellinia necat... -

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Entry
Database: EMDB / ID: EMD-3437
TitleThree-dimensional reconstruction of W1075 strain Rosellinia necatrix quadrivirus 1
Map dataReconstruction of Rosellinia necatrix quadrivirus 1 strain W1075
Sample
  • Sample: Rosellinia necatrix quadrivirus 1 full particles W1075 strain
  • Virus: Rosellinia necatrix quadrivirus 1
KeywordsdsRNA virus / quadrivirus / 3DR / fungal virus
Biological speciesRosellinia necatrix quadrivirus 1
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 8.2 Å
AuthorsLuque D / Mata CP / Gonzalez-Camacho F / Gonzalez JM / Gomez-Blanco J / Alfonso C / Rivas G / Havens WM / Kanematsu S / Suzuki N ...Luque 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
CitationJournal: J Virol / Year: 2016
Title: Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1.
Authors: 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 / ...Authors: 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 /
Abstract: Most double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids ...Most double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids help to organize the viral genome and replicative complex(es). They also act as molecular sieves that isolate the virus genome from host defense mechanisms and allow the passage of nucleotides and viral transcripts. Rosellinia necatrix quadrivirus 1 (RnQV1), the type species of the family Quadriviridae, is a dsRNA fungal virus with a multipartite genome consisting of four monocistronic segments (segments 1 to 4). dsRNA-2 and dsRNA-4 encode two CPs (P2 and P4, respectively), which coassemble into ∼450-Å-diameter capsids. We used three-dimensional cryo-electron microscopy combined with complementary biophysical techniques to determine the structures of RnQV1 virion strains W1075 and W1118. RnQV1 has a quadripartite genome, and the capsid is based on a single-shelled T=1 lattice built of P2-P4 dimers. Whereas the RnQV1-W1118 capsid is built of full-length CP, P2 and P4 of RnQV1-W1075 are cleaved into several polypeptides, maintaining the capsid structural organization. RnQV1 heterodimers have a quaternary organization similar to that of homodimers of reoviruses and other dsRNA mycoviruses. The RnQV1 capsid is the first T=1 capsid with a heterodimer as an asymmetric unit reported to date and follows the architectural principle for dsRNA viruses that a 120-subunit capsid is a conserved assembly that supports dsRNA replication and organization.
IMPORTANCE: Given their importance to health, members of the family Reoviridae are the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of ...IMPORTANCE: Given their importance to health, members of the family Reoviridae are the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of bacterial, protozoal, and fungal dsRNA viruses has improved our understanding of their structure, function, and evolution, as well. Here, we studied a dsRNA virus that infects the fungus Rosellinia necatrix, an ascomycete that is pathogenic to a wide range of plants. Using three-dimensional cryo-electron microscopy and analytical ultracentrifugation analysis, we determined the structure and stoichiometry of Rosellinia necatrix quadrivirus 1 (RnQV1). The RnQV1 capsid is a T=1 capsid with 60 heterodimers as the asymmetric units. The large amount of genetic information used by RnQV1 to construct a simple T=1 capsid is probably related to the numerous virus-host and virus-virus interactions that it must face in its life cycle, which lacks an extracellular phase.
History
DepositionMay 19, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseAug 2, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3437.jpg

Downloads & links

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Map

FileDownload / File: emd_3437.map.gz / Format: CCP4 / Size: 46.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Rosellinia necatrix quadrivirus 1 strain W1075
Voxel sizeX=Y=Z: 2.54 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-0.95905262 - 2.03882527
Average (Standard dev.)0.03592134 (±0.24132557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions232232232
Spacing232232232
CellA=B=C: 589.27997 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS232232232
D min/max/mean-0.9592.0390.036

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Supplemental data

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Sample components

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Entire : Rosellinia necatrix quadrivirus 1 full particles W1075 strain

EntireName: Rosellinia necatrix quadrivirus 1 full particles W1075 strain
Components
  • Sample: Rosellinia necatrix quadrivirus 1 full particles W1075 strain
  • Virus: Rosellinia necatrix quadrivirus 1

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Supramolecule #1000: Rosellinia necatrix quadrivirus 1 full particles W1075 strain

SupramoleculeName: Rosellinia necatrix quadrivirus 1 full particles W1075 strain
type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightExperimental: 20.6 MDa / Theoretical: 18.9 MDa / Method: Sedimentation

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Supramolecule #1: Rosellinia necatrix quadrivirus 1

SupramoleculeName: Rosellinia necatrix quadrivirus 1 / type: virus / ID: 1 / Name.synonym: RnQV1 / NCBI-ID: 1000373 / Sci species name: Rosellinia necatrix quadrivirus 1 / Sci species strain: W1075 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: RnQV1
Host (natural)Organism: Rosellinia necatrix (fungus) / Strain: W1075 / synonym: FUNGI
Molecular weightExperimental: 20.6 MDa / Theoretical: 18.9 MDa
Virus shellShell ID: 1 / Diameter: 470 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
GridDetails: R 2/2 Quantifoil grids
VitrificationCryogen name: ETHANE / 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: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
DateNov 24, 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: 423 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping & amplitude decay
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 24056

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