9TF1 | pdb_00009tf1

Structure of echovirus 18, activated particle

  • Classification: VIRUS
  • Organism(s): Echovirus E18
  • Mutation(s): No 

  • Deposited: 2025-11-26 Released: 2026-06-24 
  • Deposition Author(s): Mukhamedova, L., Plevka, P.
  • Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9TF1

This is version 1.1 of the entry. See complete history

Literature

Particles of echovirus 18 open to release their genomes in vivo.

Mukhamedova, L.Buchta, D.Trebichalska, Z.Levdansky, Y.Moravcova, J.Potesil, D.Zdrahal, Z.Hrebik, D.Nepovimova, L.Gjolberg, T.T.Andersen, J.T.Novacek, J.Fuzik, T.Plevka, P.

(2026) Proc Natl Acad Sci U S A 123: e2601182123-e2601182123

  • DOI: https://doi.org/10.1073/pnas.2601182123
  • Primary Citation Related Structures: 
    9S63, 9SPU, 9TF0, 9TF1, 9TF2

  • PubMed 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. 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.


  • Organizational Affiliation
    • Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 87.51 kDa 
  • Atom Count: 6,093 
  • Modeled Residue Count: 659 
  • Deposited Residue Count: 786 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Echovirus 18 viral protein 1287Echovirus E18Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q8V635 (Echovirus E18)
Explore Q8V635 
Go to UniProtKB:  Q8V635
Entity Groups
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UniProt GroupQ8V635
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Echovirus 18 viral protein 2260Echovirus E18Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q8V635 (Echovirus E18)
Explore Q8V635 
Go to UniProtKB:  Q8V635
Entity Groups
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UniProt GroupQ8V635
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Echovirus 18 viral protein 3239Echovirus E18Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q8V635 (Echovirus E18)
Explore Q8V635 
Go to UniProtKB:  Q8V635
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8V635
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0.0
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references