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- EMDB-17809: Tick-borne encephalitis virus Kuutsalo-14 immature virus particle -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-17809
TitleTick-borne encephalitis virus Kuutsalo-14 immature virus particle
Map dataFinal, sharpened and masked map (B factor -658.6)
Sample
  • Virus: Tick-borne encephalitis virus
Keywordsvirion / membrane protein / glycoprotein / VIRUS
Biological speciesTick-borne encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsAnastasina M / Domanska A / Pulkkinen LIA / Butcher SJ
Funding support Finland, European Union, Sweden, 8 items
OrganizationGrant numberCountry
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: To Be Published
Title: Tick-borne encephalitis virus Kuutsalo-14 immature virion
Authors: Anastasina M / Domanska A / Pulkkinen LIA / Butcher SJ
History
DepositionJul 7, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17809.png

Downloads & links

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Map

FileDownload / File: emd_17809.map.gz / Format: CCP4 / Size: 3.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal, sharpened and masked map (B factor -658.6)
Voxel sizeX=Y=Z: 1.075 Å
Density
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.27315485 - 0.7005468
Average (Standard dev.)0.0058682016 (±0.04786008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions980980980
Spacing980980980
CellA=B=C: 1053.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A

Fileemd_17809_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_17809_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 / Macromolecule list: #1-#2
Details: Virus was produced in SK-N-SH cells treated with ammonium chloride, purified, and inactivated with UV-C.
NCBI-ID: 11088 / Sci species name: Tick-borne encephalitis virus / Sci species strain: Kuutsalo-14 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 271870
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70189
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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