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- EMDB-5725: Three-dimensional Structure of Victorivirus HvV190S -

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Basic information

Entry
Database: EMDB / ID: EMD-5725
TitleThree-dimensional Structure of Victorivirus HvV190S
Map dataReconstruction of HvV190S virion
Sample
  • Sample: Helminthosporium victoriae virus 190S
  • Virus: Helminthosporium victoriae virus 190S
Biological speciesHelminthosporium victoriae virus 190S
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.1 Å
AuthorsDun SE / Li H / Cardone G / Nibert ML / Gabrial SA / Baker TS
CitationJournal: PLoS Pathog / Year: 2013
Title: Three-dimensional structure of victorivirus HvV190S suggests coat proteins in most totiviruses share a conserved core.
Authors: Sarah E Dunn / Hua Li / Giovanni Cardone / Max L Nibert / Said A Ghabrial / Timothy S Baker /
Abstract: Double-stranded (ds)RNA fungal viruses are currently assigned to six different families. Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids, 300-450 ...Double-stranded (ds)RNA fungal viruses are currently assigned to six different families. Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids, 300-450 Å in diameter. Helminthosporium victoriae virus 190S (HvV190S), prototype of recently recognized genus Victorivirus, infects the filamentous fungus Helminthosporium victoriae (telomorph: Cochliobolus victoriae), which is the causal agent of Victoria blight of oats. The HvV190S genome is 5179 bp long and encompasses two large, slightly overlapping open reading frames that encode the coat protein (CP, 772 aa) and the RNA-dependent RNA polymerase (RdRp, 835 aa). To our present knowledge, victoriviruses uniquely express their RdRps via a coupled termination-reinitiation mechanism that differs from the well-characterized Saccharomyces cerevisiae virus L-A (ScV-L-A, prototype of genus Totivirus), in which the RdRp is expressed as a CP/RdRp fusion protein due to ribosomal frameshifting. Here, we used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structures of HvV190S virions and two types of virus-like particles (capsids lacking dsRNA and capsids lacking both dsRNA and RdRp) at estimated resolutions of 7.1, 7.5, and 7.6 Å, respectively. The HvV190S capsid is thin and smooth, and contains 120 copies of CP arranged in a "T = 2" icosahedral lattice characteristic of ScV-L-A and other dsRNA viruses. For aid in our interpretations, we developed and used an iterative segmentation procedure to define the boundaries of the two, chemically identical CP subunits in each asymmetric unit. Both subunits have a similar fold, but one that differs from ScV-L-A in many details except for a core α-helical region that is further predicted to be conserved among many other totiviruses. In particular, we predict the structures of other victoriviruses to be highly similar to HvV190S and the structures of most if not all totiviruses including, Leishmania RNA virus 1, to be similar as well.
History
DepositionJul 25, 2013-
Header (metadata) releaseSep 18, 2013-
Map releaseSep 18, 2013-
UpdateSep 18, 2013-
Current statusSep 18, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 7
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5725.map.gz / Format: CCP4 / Size: 234.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of HvV190S virion
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-40.0 - 60.0
Average (Standard dev.)-0.15325418 (±5.43528509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions501501501
Spacing501501501
CellA=B=C: 536.07 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.071.071.07
M x/y/z501501501
origin x/y/z0.0000.0000.000
length x/y/z536.070536.070536.070
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS501501501
D min/max/mean-40.00060.000-0.153

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Supplemental data

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Sample components

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Entire : Helminthosporium victoriae virus 190S

EntireName: Helminthosporium victoriae virus 190S
Components
  • Sample: Helminthosporium victoriae virus 190S
  • Virus: Helminthosporium victoriae virus 190S

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Supramolecule #1000: Helminthosporium victoriae virus 190S

SupramoleculeName: Helminthosporium victoriae virus 190S / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1

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Supramolecule #1: Helminthosporium victoriae virus 190S

SupramoleculeName: Helminthosporium victoriae virus 190S / type: virus / ID: 1 / Name.synonym: HvV190S / NCBI-ID: 45237 / Sci species name: Helminthosporium victoriae virus 190S / Sci species strain: A-9 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: HvV190S
Host (natural)Organism: Cochliobolus victoriae (fungus) / synonym: FUNGI
Host systemOrganism: unidentified (others)
Virus shellShell ID: 1 / Diameter: 462 Å / T number (triangulation number): 2

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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

Concentration5 mg/mL
BufferpH: 7.8 / Details: 50 mM Tris-HCl, 5 mM EDTA, 150 mM NaCl, pH 7.8
StainingType: NEGATIVE
Details: Samples were adsorbed to continuous carbon grids that had been glow-discharged for ~25 seconds in an Emitech K350 evaporation unit. Samples were subsequently stained with 1% aqueous uranyl ...Details: Samples were adsorbed to continuous carbon grids that had been glow-discharged for ~25 seconds in an Emitech K350 evaporation unit. Samples were subsequently stained with 1% aqueous uranyl acetate and rinsed with ddH2O.
GridDetails: 200 mesh gold grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK III
Details: Vitrification carried out after applying sample to carbon-coated grids and waiting 5 minutes before inserting the grid into the Vitrobot.
Method: Blot for 3.5 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59318 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.3 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.72 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER
TemperatureMin: 90 K / Max: 92 K / Average: 91 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification using FFT
DateAug 8, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 1.09 µm / Number real images: 176 / Average electron dose: 24 e/Å2 / Bits/pixel: 8
Tilt angle min0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: ROBEM
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 20904

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