6RJF

Echovirus 1 intact particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 1EV1 - determined by Wien, M.W., Filman, D.J., Hogle, J.M.  

Literature

Extracellular Albumin and Endosomal Ions Prime Enterovirus Particles for Uncoating That Can Be Prevented by Fatty Acid Saturation.

Ruokolainen, V.Domanska, A.Laajala, M.Pelliccia, M.Butcher, S.J.Marjomaki, V.

(2019) J.Virol. 93: --

  • DOI: 10.1128/JVI.00599-19

  • PubMed Abstract: 
  • There is limited information about the molecular triggers leading to the uncoating of enteroviruses in physiological conditions. Using real-time spectroscopy and sucrose gradients with radioactively-labeled virus we show at 37 °C, formation of a low ...

    There is limited information about the molecular triggers leading to the uncoating of enteroviruses in physiological conditions. Using real-time spectroscopy and sucrose gradients with radioactively-labeled virus we show at 37 °C, formation of a low amount of albumin-triggered, metastable, uncoating intermediate of echovirus 1 without receptor engagement. This conversion was blocked by saturating the albumin with fatty acids. High potassium but low sodium and calcium concentrations, mimicking the endosomal environment, also induced the formation of a metastable uncoating intermediate of echovirus 1. Together, these factors boosted the formation of the uncoating intermediate and infectivity of this intermediate was retained, as judged by end-point titration. Cryo-electron microscopy reconstruction of the virions treated with albumin and high potassium, low sodium and low calcium concentrations resulted in a 3.6 Å resolution model revealing a fenestrated capsid showing 4 % expansion and loss of the pocket factor, similarly to altered (A-) particles described for other enteroviruses. The dimer interface between VP2 molecules was opened, the VP1 N-termini disordered and most likely externalised. The RNA was clearly visible, anchored to the capsid. The results presented here suggest that extracellular albumin, partially saturated with fatty acids, likely leads to the formation of the infectious uncoating intermediate prior to the engagement with the cellular receptor. In addition, changes in mono- and divalent cations, likely occurring in endosomes, promote capsid opening and genome release. Importance There is limited information about uncoating of enteroviruses in physiological conditions. Here, we focused on physiologically relevant factors that likely contribute to opening of echovirus 1 and other B-group enteroviruses. By combining biochemical and structural data, we show, that before entering cells, extracellular albumin is capable of priming the virus into a metastable, yet infectious intermediate state. The ionic changes that are suggested to occur in endosomes, can further contribute to uncoating and promote genome release, once the viral particle is endocytosed. Importantly, we provide a detailed high-resolution structure of a virion after treatment with albumin and a preset ion composition, showing pocket factor release, capsid expansion and fenestration, and the clearly visible genome still anchored to the capsid. This study provides valuable information about the physiological factors that contribute to the opening of B-group enteroviruses.


    Related Citations: 
    • Structure determination of echovirus 1.
      Filman, D.J.,Wien, M.W.,Cunningham, J.A.,Bergelson, J.M.,Hogle, J.M.
      (1998) Acta Crystallogr. D Biol. Crystallogr. 54: 1261
    • A pseudo-cell based approach to efficient crystallographic refinement of viruses.
      Jacobson, D.H.,Hogle, J.M.,Filman, D.J.
      (1996) Acta Crystallogr. D Biol. Crystallogr. 52: 693


    Organizational Affiliation

    Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, PO Box 35, FI-40014 Jyväskylä, Finland.,European School of Molecular Medicine (SEMM), IFOM-IEO-Campus, via Adamello 16, Milan 20139, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
1
281Echovirus 1 (strain Human/Egypt/Farouk/1951)Mutation(s): 0 
Find proteins for O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Go to UniProtKB:  O91734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP2
2
261Echovirus 1 (strain Human/Egypt/Farouk/1951)Mutation(s): 0 
Find proteins for O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Go to UniProtKB:  O91734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
3
239Echovirus 1 (strain Human/Egypt/Farouk/1951)Mutation(s): 0 
Find proteins for O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Go to UniProtKB:  O91734
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
4
68N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download SDF File 
Download CCD File 
1
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland275199
Academy of FinlandFinland315950
Sigrid Juselius FoundationFinland--
Jane and Aatos Erkko FoundationFinland--

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references
  • Version 1.2: 2019-08-21
    Type: Data collection, Database references