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- EMDB-3619: RnQV1-W1118 empty capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-3619
TitleRnQV1-W1118 empty capsid
Map dataRosellinia necatrix quadrivirus 1 strain W1118 (RnQV1-1118), empty particle
Sample
  • Virus: Rosellinia necatrix quadrivirus 1
Function / homologyCapsid protein / Capsid protein
Function and homology information
Biological speciesRosellinia necatrix quadrivirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMata CP / Luque D / Gomez-Blanco J / Rodriguez JM / Suzuki N / Ghabrial SA / Carrascosa JL / Trus BL / Caston JR
CitationJournal: PLoS Pathog / Year: 2017
Title: Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses.
Authors: Carlos P Mata / Daniel Luque / Josué Gómez-Blanco / Javier M Rodríguez / José M González / Nobuhiro Suzuki / Said A Ghabrial / José L Carrascosa / Benes L Trus / José R Castón /
Abstract: Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3. ...Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues. Despite a lack of sequence similarity between the two proteins, they have a similar α-helical domain, the structural signature shared with the lineage of the dsRNA bluetongue virus-like viruses. Domain insertions in P2 and P4 preferential sites provide additional functions at the capsid outer surface, probably related to enzyme activity. The P2 insertion has a fold similar to that of gelsolin and profilin, two actin-binding proteins with a function in cytoskeleton metabolism, whereas the P4 insertion suggests protease activity involved in cleavage of the P2 383-residue C-terminal region, absent in the mature viral particle. Our results indicate that the intimate virus-fungus partnership has altered the capsid genome-protective and/or receptor-binding functions. Fungal virus evolution has tended to allocate enzyme activities to the virus capsid outer surface.
History
DepositionMar 7, 2017-
Header (metadata) releaseApr 19, 2017-
Map releaseNov 29, 2017-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • 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
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5nd1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3619.png

Downloads & links

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Map

FileDownload / File: emd_3619.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRosellinia necatrix quadrivirus 1 strain W1118 (RnQV1-1118), empty particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.852351 - 1.370603
Average (Standard dev.)0.0006925482 (±0.09049471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 °

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
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
Components
  • Virus: Rosellinia necatrix quadrivirus 1

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Supramolecule #1: Rosellinia necatrix quadrivirus 1

SupramoleculeName: Rosellinia necatrix quadrivirus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1000373 / Sci species name: Rosellinia necatrix quadrivirus 1 / Sci species strain: W1118 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Rosellinia necatrix (fungus)
Molecular weightExperimental: 15.9 MDa
Virus shellShell ID: 1 / Name: P2 and P4 / Diameter: 470.0 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8 / Details: 50 mM Tris-HCl pH 7.8, 150 mM NaCl, 5 mM EDTA
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 4-21 / Number real images: 1125 / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 0.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 53683
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

3438

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 37531
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 15000 / Software - Name: RELION (ver. 1.4)

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-5nd1:
Viral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus

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