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- EMDB-3350: Electron cryo-microscopy of an dsRNA-empty totivirus-like Omono R... -

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Basic information

Entry
Database: EMDB / ID: EMD-3350
TitleElectron cryo-microscopy of an dsRNA-empty totivirus-like Omono River virus (OmRV)
Map dataReconstruction of empty OmRV
Sample
  • Sample: Totivirus-like Omono River virus (OmRV)
  • Virus: Omono River virus
KeywordsVirus / totivirus / mosquito / totiviridae / double-stranded RNA / dsRNA / capsid / icosahedral / icosahedron / T=1
Biological speciesOmono River virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsOkamoto K / Miyazaki N / Larsson DSD / Kobayashi D / Svenda M / Muehlig K / Maia FRNC / Gunn LH / Isawa H / Kobayashi M ...Okamoto K / Miyazaki N / Larsson DSD / Kobayashi D / Svenda M / Muehlig K / Maia FRNC / Gunn LH / Isawa H / Kobayashi M / Sawabe K / Murata K / Hajdu J
CitationJournal: Sci Rep / Year: 2016
Title: The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes.
Authors: Kenta Okamoto / Naoyuki Miyazaki / Daniel S D Larsson / Daisuke Kobayashi / Martin Svenda / Kerstin Mühlig / Filipe R N C Maia / Laura H Gunn / Haruhiko Isawa / Mutsuo Kobayashi / Kyoko ...Authors: Kenta Okamoto / Naoyuki Miyazaki / Daniel S D Larsson / Daisuke Kobayashi / Martin Svenda / Kerstin Mühlig / Filipe R N C Maia / Laura H Gunn / Haruhiko Isawa / Mutsuo Kobayashi / Kyoko Sawabe / Kazuyoshi Murata / Janos Hajdu /
Abstract: Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper ...Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short "plug" structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.
History
DepositionMar 1, 2016-
Header (metadata) releaseMar 9, 2016-
Map releaseSep 28, 2016-
UpdateSep 28, 2016-
Current statusSep 28, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD3350-500p...

Downloads & links

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Map

FileDownload / File: emd_3350.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of empty OmRV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 280 pix.
= 526.4 Å		1.88 Å/pix.
x 280 pix.
= 526.4 Å		1.88 Å/pix.
x 280 pix.
= 526.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.07970962 - 0.55625087
Average (Standard dev.)0.00878616 (±0.03463331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 526.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.881.881.88
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z526.400526.400526.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0800.5560.009

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Supplemental data

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Sample components

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Entire : Totivirus-like Omono River virus (OmRV)

EntireName: Totivirus-like Omono River virus (OmRV)
Components
  • Sample: Totivirus-like Omono River virus (OmRV)
  • Virus: Omono River virus

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Supramolecule #1000: Totivirus-like Omono River virus (OmRV)

SupramoleculeName: Totivirus-like Omono River virus (OmRV) / type: sample / ID: 1000 / Oligomeric state: T=1 (T=2) / Number unique components: 1

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Supramolecule #1: Omono River virus

SupramoleculeName: Omono River virus / type: virus / ID: 1 / NCBI-ID: 753758 / Sci species name: Omono River virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Culex mosquito / Strain: AK4 / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Name: Capsid / Diameter: 61 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

Concentration1.43 mg/mL
BufferpH: 7.5 / Details: 100 mM ammonium acetate
GridDetails: Holey carbon grid
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: Omega
DateNov 19, 2014
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: JEOL

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 12207

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