6GV4

High-resolution Cryo-EM of Fab-labeled human parechovirus 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

A 2.8-Angstrom-Resolution Cryo-Electron Microscopy Structure of Human Parechovirus 3 in Complex with Fab from a Neutralizing Antibody.

Domanska, A.Flatt, J.W.Jukonen, J.J.J.Geraets, J.A.Butcher, S.J.

(2019) J.Virol. 93: --

  • DOI: 10.1128/JVI.01597-18

  • PubMed Abstract: 
  • Human parechovirus 3 (HPeV3) infection is associated with sepsis characterized by significant immune activation and subsequent tissue damage in neonates. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tool ...

    Human parechovirus 3 (HPeV3) infection is associated with sepsis characterized by significant immune activation and subsequent tissue damage in neonates. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and the lack of a vaccine or specific antiviral therapy. Toward the latter, we present a 2.8-Å-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody, AT12-015, using cryo-electron microscopy (cryo-EM) and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally, at high resolution, it was possible to model a stretch of RNA inside the virion and, from this, identify the key features that drive and stabilize protein-RNA association during assembly. IMPORTANCE Human parechovirus 3 (HPeV3) is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, for which, despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Toward this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high resolution, it was possible to precisely define the epitope that, when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interactions and viral pathogenesis mechanisms and for finding potential cures for infection and disease.


    Organizational Affiliation

    Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland ausra.domanska@helsinki.fi sarah.butcher@helsinki.fi.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP0
A
289Human parechovirus 3Mutation(s): 0 
Find proteins for Q8BES5 (Human parechovirus 3)
Go to UniProtKB:  Q8BES5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP1
B
229Human parechovirus 3Mutation(s): 0 
Find proteins for Q8BES5 (Human parechovirus 3)
Go to UniProtKB:  Q8BES5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP3
C
256Human parechovirus 3Mutation(s): 0 
Find proteins for A0A291FGQ4 (Human parechovirus 3)
Go to UniProtKB:  A0A291FGQ4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
AT12-015 antibody variable heavy
H
121N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
AT12-015 antibody variable light
L
113N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*GP*UP*AP*UP*UP*U)-3')D8Human parechovirus 3
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 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
European UnionPIEF-GA-2013-628150
European UnionPIAPP-GA-2013-612308
European Union653706

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Data collection, Database references
  • Version 1.3: 2019-04-03
    Type: Data collection, Database references
  • Version 2.0: 2019-06-26
    Type: Atomic model, Data collection, Database references