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- EMDB-16440: C1 reconstruction of Tanay virus particle -

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Basic information

Entry
Database: EMDB / ID: EMD-16440
TitleC1 reconstruction of Tanay virus particle
Map dataC1 reconstruction of TANAV particle
Sample
  • Virus: Tanay virus
KeywordsMosquito virus / Negevirus / Envelope / VIRUS
Biological speciesTanay virus
Methodsingle particle reconstruction / cryo EM / Resolution: 23.6 Å
AuthorsOkamoto K / Song C / Miyazaki N / Murata K
Funding support Sweden, Japan, 3 items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Swedish Research Council2018-00421 Sweden
Ministry of Education, Culture, Sports, Science and Technology (Japan)25251009 Japan
CitationJournal: J Gen Virol / Year: 2023
Title: Structure and its transformation of elliptical nege-like virus Tanay virus.
Authors: Kenta Okamoto / Chihong Song / Han Wang / Miako Sakaguchi / Christina Chalkiadaki / Naoyuki Miyazaki / Takeshi Nabeshima / Kouichi Morita / Shingo Inoue / Kazuyoshi Murata /
Abstract: Negeviruses that infect insects are recently identified virus species that are phylogenetically related to several plant viruses. They exhibit a unique virion structure, an elliptical core with a ...Negeviruses that infect insects are recently identified virus species that are phylogenetically related to several plant viruses. They exhibit a unique virion structure, an elliptical core with a short projection. Negeviruses encode two structural proteins, a glycoprotein that forms a short projection, and an envelope protein that forms an elliptical core. The glycoprotein has been reported only in the negeviruses' genes, and not in phylogenetically related plant viruses' genes. In this report, we first describe the three-dimensional electron cryo-microscopy (cryo-EM) structure of Tanay virus (TANAV), one of the nege-like viruses. TANAV particle demonstrates a periodical envelope structure consisting of three layers surrounding the centred viral RNA. The elliptical core dynamically changes its shape under acidic and even low detergent conditions to form bullet-like or tubular shapes. The further cryo-EM studies on these transformed TANAV particles reveal their overall structural rearrangement. These findings suggest putative geometries of TANAV and its transformation in the life cycle, and the potential importance of the short projection for enabling cell entry to the insect hosts.
History
DepositionJan 10, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16440.png

Downloads & links

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Map

FileDownload / File: emd_16440.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC1 reconstruction of TANAV particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.99 Å/pix.
x 400 pix.
= 796.8 Å		1.99 Å/pix.
x 400 pix.
= 796.8 Å		1.99 Å/pix.
x 400 pix.
= 796.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.992 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0133
Minimum - Maximum-0.027982712 - 0.095500946
Average (Standard dev.)0.0019177055 (±0.013311569)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 796.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map1

Fileemd_16440_half_map_1.map
AnnotationHalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map2

Fileemd_16440_half_map_2.map
AnnotationHalf-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tanay virus

EntireName: Tanay virus
Components
  • Virus: Tanay virus

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Supramolecule #1: Tanay virus

SupramoleculeName: Tanay virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1489714 / Sci species name: Tanay virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10282
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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