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- EMDB-54510: Echovirus 18 particle missing two pentamers in situ, asymmetric r... -

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Basic information

Entry
Database: EMDB / ID: EMD-54510
TitleEchovirus 18 particle missing two pentamers in situ, asymmetric reconstruction
Map dataMain map
Sample
  • Virus: Echovirus E18
KeywordsVirus / in situ structure
Biological speciesEchovirus E18
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsMukhamedova L / Plevka P / Trebichalska Z / Novacek J
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Particles of echovirus 18 open to release their genomes in vivo.
Authors: Liya Mukhamedova / David Buchta / Zuzana Trebichalská / Yevgen Levdansky / Jana Moravcová / David Potěšil / Zbyněk Zdráhal / Dominik Hrebík / Lucie Nepovímová / Torleif Tollefsrud ...Authors: Liya Mukhamedova / David Buchta / Zuzana Trebichalská / Yevgen Levdansky / Jana Moravcová / David Potěšil / Zbyněk Zdráhal / Dominik Hrebík / Lucie Nepovímová / Torleif Tollefsrud Gjølberg / Jan Terje Andersen / Jiří Nováček / Tibor Füzik / Pavel Plevka /
Abstract: Enteroviruses cause a broad spectrum of human diseases, ranging from mild respiratory or gastrointestinal infections to severe neurological disorders such as aseptic meningitis and encephalitis. ...Enteroviruses cause a broad spectrum of human diseases, ranging from mild respiratory or gastrointestinal infections to severe neurological disorders such as aseptic meningitis and encephalitis. Enterovirus cell entry involves receptor-mediated endocytosis followed by destabilizing rearrangements of the virus capsid that enable genome release. However, the mechanism of enterovirus genome release has not been visualized in infected cells. Here, we used cryoelectron tomography and microscopy to image echovirus 18 (E18) entry into host cells and its interaction with the neonatal Fc receptor (FcRn). 30 min postinfection, endosomes and cytoplasm contained empty capsids missing one or several pentamers of capsid proteins, providing evidence that in vivo E18 releases its genome through capsid opening. In vitro, FcRn binding induced the expulsion of pocket factors from hydrophobic pockets in VP1, priming the virus for uncoating. The cryoelectron microscopy reconstruction of genome-containing particles of E18 inside infected cells did not reveal pocket factors, indicating that receptor binding triggers the same priming process during infection. We did not detect activated particles in infected cells, suggesting that these intermediates are short-lived and rapidly release their genomes in vivo. Our results identify capsid opening as the in vivo mechanism of echovirus 18 genome release, providing structural evidence for a process previously only inferred from in vitro experiments.
History
DepositionJul 22, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54510.png

Downloads & links

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Map

FileDownload / File: emd_54510.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.08 Å/pix.
x 256 pix.
= 532.6 Å		2.08 Å/pix.
x 256 pix.
= 532.6 Å		2.08 Å/pix.
x 256 pix.
= 532.6 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.08047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.3108994 - 0.9076697
Average (Standard dev.)0.009092692 (±0.10400625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 532.60034 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54510_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half A

Fileemd_54510_half_map_1.map
AnnotationHalf A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_54510_half_map_2.map
AnnotationHalf B
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Sample components

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Entire : Echovirus E18

EntireName: Echovirus E18
Components
  • Virus: Echovirus E18

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Supramolecule #1: Echovirus E18

SupramoleculeName: Echovirus E18 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 47506 / Sci species name: Echovirus E18 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.9 MDa
Virus shellShell ID: 1 / Diameter: 330.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1290 / Average exposure time: 8.0 sec. / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hbk

Final reconstructionNumber classes used: 5 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 6365
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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