5APM

Multiple capsid-stabilizing protein-RNA and protein-protein interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Multiple Capsid-Stabilizing Interactions Revealed in a High-Resolution Structure of an Emerging Picornavirus Causing Neonatal Sepsis

Shakeel, S.Westerhuis, B.M.Domanska, A.Koning, R.I.Matadeen, R.Koster, A.J.Bakker, A.Q.Beaumont, T.Wolthers, K.C.Butcher, S.J.

(2016) Nat Commun 7: 11387

  • DOI: https://doi.org/10.1038/ncomms11387
  • Primary Citation of Related Structures:  
    5APM

  • PubMed Abstract: 

    The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA-protein interactions and dissection of virus assembly on the basis of RNA nucleation.


  • Organizational Affiliation

    Institute of Biotechnology and Department of Biological Sciences, Viikinkaari 1, 00014 University of Helsinki, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1198Human parechovirus 3Mutation(s): 0 
UniProt
Find proteins for D2IE17 (Human parechovirus 3)
Explore D2IE17 
Go to UniProtKB:  D2IE17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2IE17
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP3237Human parechovirus 3Mutation(s): 0 
UniProt
Find proteins for D2IE17 (Human parechovirus 3)
Explore D2IE17 
Go to UniProtKB:  D2IE17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2IE17
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP0263Human parechovirus 3Mutation(s): 0 
UniProt
Find proteins for D2IE17 (Human parechovirus 3)
Explore D2IE17 
Go to UniProtKB:  D2IE17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2IE17
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONAuto3DEM
RECONSTRUCTIONEMAN1
RECONSTRUCTIONEMAN2
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations