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- PDB-9s63: Echovirus 18 in situ, virion, I4 -

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Basic information

Entry
Database: PDB / ID: 9s63
TitleEchovirus 18 in situ, virion, I4
Components
  • Echovirus 18 viral protein 2
  • Echovirus 18 viral protein 3
  • Echovirus 18 viral protein 4
  • Genome polyprotein
KeywordsVIRUS / in situ structure
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / virion attachment to host cell / host cell nucleus / structural molecule activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEchovirus E18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMukhamedova, L. / Plevka, P. / Trebichalska, Z. / Novacek, J.
Funding supportEuropean Union, 1items
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 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Echovirus 18 viral protein 2
C: Echovirus 18 viral protein 3
D: Echovirus 18 viral protein 4


Theoretical massNumber of molelcules
Total (without water)94,9864
Polymers94,9864
Non-polymers00
Water00
1
A: Genome polyprotein
B: Echovirus 18 viral protein 2
C: Echovirus 18 viral protein 3
D: Echovirus 18 viral protein 4
x 60


Theoretical massNumber of molelcules
Total (without water)5,699,153240
Polymers5,699,153240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Genome polyprotein


Mass: 32564.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Echovirus 18 viral protein 2


Mass: 28802.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Echovirus 18 viral protein 3


Mass: 26143.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Echovirus 18 viral protein 4


Mass: 7475.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Echovirus E18 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
117.9 MDaNO
217.9 MDaNO
Source (natural)Organism: Echovirus E18
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 330 nm
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 34 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1290
EM imaging opticsPhase plate: OTHER

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1337 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6hbk

6hbk


Accession code: 6hbk / Source name: PDB / Type: experimental model

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