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- EMDB-2933: Cryo-EM single particle reconstruction of Rosellinia necatrix meg... -

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Basic information

Entry
Database: EMDB / ID: EMD-2933
TitleCryo-EM single particle reconstruction of Rosellinia necatrix megabirnavirus 1 reconstructed with the mixture of empty and full particles
Map dataReconstruction of RnMBV1
Sample
  • Sample: Rosellinia necatrix megabirnavirus 1
  • Virus: Rosellinia necatrix megabirnavirus 1
KeywordsVirus / fungal virus
Biological speciesRosellinia necatrix megabirnavirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 11.6 Å
AuthorsMiyazaki N / Salaipeth L / Kanematsu S / Iwasaki K / Suzuki N
CitationJournal: J Gen Virol / Year: 2015
Title: Megabirnavirus structure reveals a putative 120-subunit capsid formed by asymmetrical dimers with distinctive large protrusions.
Authors: Naoyuki Miyazaki / Lakha Salaipeth / Satoko Kanematsu / Kenji Iwasaki / Nobuhiro Suzuki /
Abstract: Rosellinia necatrix megabirnavirus 1 (RnMBV1) W779 is a bi-segmented dsRNA virus and a strain of the type species Rosellinia necatrix megabirnavirus 1 of the family Megabirnaviridae. RnMBV1 causes ...Rosellinia necatrix megabirnavirus 1 (RnMBV1) W779 is a bi-segmented dsRNA virus and a strain of the type species Rosellinia necatrix megabirnavirus 1 of the family Megabirnaviridae. RnMBV1 causes severe reduction of both mycelial growth of Rosellinia necatrix in synthetic medium and fungal virulence to plant hosts, and thus has strong potential for virocontrol (biological control using viruses) of white rot. The structure of RnMBV1 was examined by cryo-electron microscopy and three-dimensional reconstruction at 15.7 Å resolution. The diameter of the RnMBV1 capsid was 520 Å, and the capsid was composed of 60 asymmetrical dimers in the T = 1 (so-called T = 2) lattice that is well conserved among dsRNA viruses. However, RnMBV1 has putatively 120 large protrusions with a width of ∼ 45 Å and a height of ∼ 50 Å on the virus surface, making it distinguishable from the other dsRNA viruses.
History
DepositionMar 13, 2015-
Header (metadata) releaseMay 6, 2015-
Map releaseApr 13, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.99
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.99
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2933.png

Downloads & links

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Map

FileDownload / File: emd_2933.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of RnMBV1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 400 pix.
= 712. Å		1.78 Å/pix.
x 400 pix.
= 712. Å		1.78 Å/pix.
x 400 pix.
= 712. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.99 / Movie #1: 0.99
Minimum - Maximum-1.80275977 - 3.4028976
Average (Standard dev.)0.10547384 (±0.43454188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 712.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z712.000712.000712.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-1.8033.4030.105

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Supplemental data

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Sample components

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Entire : Rosellinia necatrix megabirnavirus 1

EntireName: Rosellinia necatrix megabirnavirus 1
Components
  • Sample: Rosellinia necatrix megabirnavirus 1
  • Virus: Rosellinia necatrix megabirnavirus 1

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Supramolecule #1000: Rosellinia necatrix megabirnavirus 1

SupramoleculeName: Rosellinia necatrix megabirnavirus 1 / type: sample / ID: 1000 / Oligomeric state: 120 subunits / Number unique components: 1
Molecular weightExperimental: 16.2 MDa / Theoretical: 16.2 MDa

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Supramolecule #1: Rosellinia necatrix megabirnavirus 1

SupramoleculeName: Rosellinia necatrix megabirnavirus 1 / type: virus / ID: 1 / Name.synonym: RnMBV1 / NCBI-ID: 1285598 / Sci species name: Rosellinia necatrix megabirnavirus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: RnMBV1
Host (natural)Organism: Rosellinia necatrix (fungus) / Strain: W779 / synonym: FUNGI
Molecular weightTheoretical: 16.2 MDa
Virus shellShell ID: 1 / Diameter: 520 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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateApr 18, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 11.6 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 2502

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