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- EMDB-14516: Tick-Borne Encephalitis virus Kuutsalo-14 -

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Basic information

Entry
Database: EMDB / ID: EMD-14516
TitleTick-Borne Encephalitis virus Kuutsalo-14
Map data
Sample
  • Virus: Tick-borne encephalitis virus
Keywordsvirion / membrane protein / glycoprotein / VIRUS
Biological speciesTick-borne encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPulkkinen LIA / Barrass SV / Anastasina M / Butcher SJ
Funding support Finland, European Union, Sweden, 9 items
OrganizationGrant numberCountry
University of Helsinki Finland
University of Helsinki Finland
University of Helsinki Research Foundation Finland
H2020 Marie Curie Actions of the European Commission799929European Union
H2020 Marie Curie Actions of the European Commission765042European Union
Swedish Research Council2018-05851 Sweden
Academy of Finland315950 Finland
Sigrid Juselius Foundation95-7202-38 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Viruses / Year: 2022
Title: Molecular Organisation of Tick-Borne Encephalitis Virus.
Authors: Lauri I A Pulkkinen / Sarah V Barrass / Aušra Domanska / Anna K Överby / Maria Anastasina / Sarah J Butcher /
Abstract: Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family . Structural studies of flavivirus virions have primarily focused on mosquito-borne species, ...Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family . Structural studies of flavivirus virions have primarily focused on mosquito-borne species, with only one cryo-electron microscopy (cryo-EM) structure of a tick-borne species published. Here, we present a 3.3 Å cryo-EM structure of the TBEV virion of the Kuutsalo-14 isolate, confirming the overall organisation of the virus. We observe conformational switching of the peripheral and transmembrane helices of M protein, which can explain the quasi-equivalent packing of the viral proteins and highlights their importance in stabilising membrane protein arrangement in the virion. The residues responsible for M protein interactions are highly conserved in TBEV but not in the structurally studied Hypr strain, nor in mosquito-borne flaviviruses. These interactions may compensate for the lower number of hydrogen bonds between E proteins in TBEV compared to the mosquito-borne flaviviruses. The structure reveals two lipids bound in the E protein which are important for virus assembly. The lipid pockets are comparable to those recently described in mosquito-borne Zika, Spondweni, Dengue, and Usutu viruses. Our results thus advance the understanding of tick-borne flavivirus architecture and virion-stabilising interactions.
History
DepositionMar 8, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14516.png

Downloads & links

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Map

FileDownload / File: emd_14516.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 720 pix.
= 590.4 Å		0.82 Å/pix.
x 720 pix.
= 590.4 Å		0.82 Å/pix.
x 720 pix.
= 590.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0034894934 - 0.008967523
Average (Standard dev.)-0.00002518198 (±0.000797002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 590.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14516_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_14516_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14516_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Tick-borne encephalitis virus

EntireName: Tick-borne encephalitis virus
Components
  • Virus: Tick-borne encephalitis virus

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Supramolecule #1: Tick-borne encephalitis virus

SupramoleculeName: Tick-borne encephalitis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11084 / Sci species name: Tick-borne encephalitis 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: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15150
FSC plot (resolution estimation)

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