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- EMDB-55316: Asymmetric reconstruction of TBEV virion -

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Basic information

Entry
Database: EMDB / ID: EMD-55316
TitleAsymmetric reconstruction of TBEV virion
Map dataAsymmetric reconstruction of TBEV virion - main map
Sample
  • Virus: Tick-borne encephalitis virus
Keywordstick borne encephalitis virus / envelope / flavivirus / spike / VIRUS / asymmetric / mature particle
Biological speciesTick-borne encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 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: Sci Adv / Year: 2026
Title: Structures of asymmetric particles of tick-borne encephalitis virus provide insight into flavivirus assembly and maturation.
Authors: Tibor Füzik / Maria Anastasina / Peter Pajtinka / Ausra Domanska / Lauri I A Pulkkinen / Lenka Šmerdová / Lucie Nepovímová / Petra Formanová-Pokorná / Petra Straková / Jiří ...Authors: Tibor Füzik / Maria Anastasina / Peter Pajtinka / Ausra Domanska / Lauri I A Pulkkinen / Lenka Šmerdová / Lucie Nepovímová / Petra Formanová-Pokorná / Petra Straková / Jiří Nováček / Daniel Růžek / Robert Vácha / Sarah J Butcher / Pavel Plevka /
Abstract: Flaviviruses are globally distributed human pathogens. However, the mechanisms underlying flavivirus assembly and maturation remain poorly understood. Here, we show that many particles of tick-borne ...Flaviviruses are globally distributed human pathogens. However, the mechanisms underlying flavivirus assembly and maturation remain poorly understood. Here, we show that many particles of tick-borne encephalitis virus (TBEV) are asymmetric and lack subsets of surface heterodimers. Immature particles of TBEV contain incomplete spikes, providing evidence that their coats assemble directly from heterodimers of premembrane (prM) and envelope (E) proteins. Exposure of TBEV particles to acidic pH in the Golgi complex promotes maturation. The spikes and herringbone regions in TBEV maturation intermediates are oriented randomly rather than conforming to a common icosahedral symmetry. Consequently, the mature herringbone lattice forms around a randomly oriented nucleation center, expanding by addition of membrane-envelope heterodimers as the spikes disassemble and prMs are cleaved. The observed incompleteness of the protein coats explains, as an alternative to particle breathing, how flaviviruses can be neutralized by antibodies that bind to regions of E proteins normally inaccessible in the spiky or herringbone structures.
History
DepositionOct 7, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55316.png

Downloads & links

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Map

FileDownload / File: emd_55316.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of TBEV virion - main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.55 Å/pix.
x 256 pix.
= 653.542 Å		2.55 Å/pix.
x 256 pix.
= 653.542 Å		2.55 Å/pix.
x 256 pix.
= 653.542 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5529 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0285
Minimum - Maximum-0.10122675 - 0.19609389
Average (Standard dev.)0.005416068 (±0.01391473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 653.5424 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55316_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 TBEV virion - half map 1

Fileemd_55316_half_map_1.map
AnnotationAsymmetric reconstruction of TBEV virion - half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Asymmetric reconstruction of TBEV virion - half map 1

Fileemd_55316_half_map_2.map
AnnotationAsymmetric reconstruction of TBEV virion - 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: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / 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: 13122 / Average exposure time: 2.0 sec. / Average electron dose: 48.0 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

Particle selectionNumber selected: 162541
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: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 73881
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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