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- EMDB-15857: Rosellinia necatrix megabirnavirus 1-W779 empty capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-15857
TitleRosellinia necatrix megabirnavirus 1-W779 empty capsid
Map data
Sample
  • Virus: Rosellinia necatrix megabirnavirus 1/W779
Biological speciesRosellinia necatrix megabirnavirus 1/W779
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang H / Okamoto K / Miyazaki N / Suzuki N
Funding support Sweden, Japan, 2 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: PLoS Pathog / Year: 2023
Title: Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture.
Authors: Han Wang / Lakha Salaipeth / Naoyuki Miyazaki / Nobuhiro Suzuki / Kenta Okamoto /
Abstract: Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces ...Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Compared with other non-enveloped icosahedral dsRNA viruses, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus.
History
DepositionSep 21, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15857.png

Downloads & links

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Map

FileDownload / File: emd_15857.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 580 pix.
= 649.6 Å		1.12 Å/pix.
x 580 pix.
= 649.6 Å		1.12 Å/pix.
x 580 pix.
= 649.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.101
Minimum - Maximum-0.19032802 - 0.32027513
Average (Standard dev.)0.00010662195 (±0.02129223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-290-290-290
Dimensions580580580
Spacing580580580
CellA=B=C: 649.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15857_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15857_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Rosellinia necatrix megabirnavirus 1/W779

EntireName: Rosellinia necatrix megabirnavirus 1/W779
Components
  • Virus: Rosellinia necatrix megabirnavirus 1/W779

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Supramolecule #1: Rosellinia necatrix megabirnavirus 1/W779

SupramoleculeName: Rosellinia necatrix megabirnavirus 1/W779 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 658904 / Sci species name: Rosellinia necatrix megabirnavirus 1/W779 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14602

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