6GV4

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 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
  • Primary Citation of Related Structures:  
    6GV4

  • 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 tools for early detection and the lack of a vaccine or specific antiviral therapy ...

    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.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VP0B [auth A]289Human parechovirus 3Mutation(s): 0 
UniProt
Find proteins for Q8BES5 (Human parechovirus 3)
Explore Q8BES5 
Go to UniProtKB:  Q8BES5
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VP1C [auth B]229Human parechovirus 3Mutation(s): 0 
UniProt
Find proteins for Q8BES5 (Human parechovirus 3)
Explore Q8BES5 
Go to UniProtKB:  Q8BES5
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
VP3D [auth C]256Human parechovirus 3Mutation(s): 0 
UniProt
Find proteins for A0A291FGQ4 (Human parechovirus 3)
Explore A0A291FGQ4 
Go to UniProtKB:  A0A291FGQ4
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
AT12-015 antibody variable heavyE [auth H]121Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
AT12-015 antibody variable lightF [auth L]113Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*GP*GP*UP*AP*UP*UP*U)-3')A [auth D]8Human parechovirus 3
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    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  (Full details and data files)

    • Version 1.0: 2018-11-21
      Type: Initial release
    • Version 1.1: 2018-12-05
      Changes: Data collection, Database references
    • Version 1.2: 2019-02-20
      Changes: Data collection, Database references
    • Version 1.3: 2019-04-03
      Changes: Data collection, Database references
    • Version 2.0: 2019-06-26
      Changes: Atomic model, Data collection, Database references
    • Version 2.1: 2020-07-29
      Changes: Data collection