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- EMDB-55314: Asymmetric reconstruction of immature TBEV particle with 2 irregu... -

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Basic information

Entry
Database: EMDB / ID: EMD-55314
TitleAsymmetric reconstruction of immature TBEV particle with 2 irregularities
Map dataAsymmetric reconstruction of immature TBEV particle with 2 irregularities - main map
Sample
  • Virus: Tick-borne encephalitis virus
Keywordstick borne encephalitis virus / envelope / flavivirus / spike / VIRUS / asymmetric / immature particle
Biological speciesTick-borne encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 10.25 Å
AuthorsFuzikt T / Plevka P / Smerdova L / Nepovimova L
Funding support Czech Republic, European Union, Sweden, Finland, 7 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2023050 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
European Research Council (ERC)101043452European Union
Swedish Research Council2018-05851 Sweden
Academy of Finland315950 Finland
Sigrid Juselius Foundation95-7202-38 Finland
CitationJournal: To Be Published
Title: Structures of asymmetric particles of TBEV provide insight into flavivirus assembly and maturation
Authors: Fuzik T / Anastasina M / Pajtinka P / Domanska A / Pulkkinen LIA / Smerdova L / Nepovimova L / Formanova-Pokorna P / Strakova P / Novacek J / Ruzek D / Vacha R / Butcher SJ / Plevka P
History
DepositionOct 7, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55314.png

Downloads & links

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Map

FileDownload / File: emd_55314.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of immature TBEV particle with 2 irregularities - main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 512 pix.
= 800.256 Å		1.56 Å/pix.
x 512 pix.
= 800.256 Å		1.56 Å/pix.
x 512 pix.
= 800.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.563 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00736
Minimum - Maximum-0.005899097 - 0.035660584
Average (Standard dev.)0.0013684551 (±0.0038060693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 800.256 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55314_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Asymmetric reconstruction of immature TBEV particle with 2...

Fileemd_55314_half_map_1.map
AnnotationAsymmetric reconstruction of immature TBEV particle with 2 irregularities - half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Asymmetric reconstruction of immature TBEV particle with 2...

Fileemd_55314_half_map_2.map
AnnotationAsymmetric reconstruction of immature TBEV particle with 2 irregularities - half map 1
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 / NCBI-ID: 11084 / Sci species name: Tick-borne encephalitis virus / Sci species strain: Neudoerfl / Virus type: VIRION / Virus isolate: OTHER / 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

Concentration2 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
20.0 mMTristrisaminomethane
120.0 mMNaClsodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid

Details: pH adjusted at 4 deg Celsius
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11246 / Average exposure time: 2.0 sec. / Average electron dose: 44.0 e/Å2 / Details: fractionated into 40 fractions
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Details: Stochastic gradient descent generated initial model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 13214
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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