4Z92

crystal structure of parechovirus-1 virion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Work: 0.290 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Structure of Human Parechovirus 1 Reveals an Association of the RNA Genome with the Capsid.

Kalynych, S.Palkova, L.Plevka, P.

(2015) J Virol 90: 1377-1386

  • DOI: 10.1128/JVI.02346-15
  • Primary Citation of Related Structures:  
    4Z92

  • PubMed Abstract: 
  • Parechoviruses are human pathogens that cause diseases ranging from gastrointestinal disorders to encephalitis. Unlike those of most picornaviruses, parechovirus capsids are composed of only three subunits: VP0, VP1, and VP3. Here, we present the structure of a human parechovirus 1 (HPeV-1) virion determined to a resolution of 3 ...

    Parechoviruses are human pathogens that cause diseases ranging from gastrointestinal disorders to encephalitis. Unlike those of most picornaviruses, parechovirus capsids are composed of only three subunits: VP0, VP1, and VP3. Here, we present the structure of a human parechovirus 1 (HPeV-1) virion determined to a resolution of 3.1 Å. We found that interactions among pentamers in the HPeV-1 capsid are mediated by the N termini of VP0s, which correspond to the capsid protein VP4 and the N-terminal part of the capsid protein VP2 of other picornaviruses. In order to facilitate delivery of the virus genome into the cytoplasm, the N termini of VP0s have to be released from contacts between pentamers and exposed at the particle surface, resulting in capsid disruption. A hydrophobic pocket, which can be targeted by capsid-binding antiviral compounds in many other picornaviruses, is not present in HPeV-1. However, we found that interactions between the HPeV-1 single-stranded RNA genome and subunits VP1 and VP3 in the virion impose a partial icosahedral ordering on the genome. The residues involved in RNA binding are conserved among all parechoviruses, suggesting a putative role of the genome in virion stability or assembly. Therefore, putative small molecules that could disrupt HPeV RNA-capsid protein interactions could be developed into antiviral inhibitors.


    Organizational Affiliation

    Central European Institute of Technology, Masaryk University, Brno, Czech Republic pavel.plevka@ceitec.muni.cz.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
capsid subunit VP1A234Echovirus 22 (strain Harris)Mutation(s): 0 
EC: 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 3.4.22.29 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q66578 (Human parechovirus 1 (strain Harris))
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Go to UniProtKB:  Q66578
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid subunit VP3B253Echovirus 22 (strain Harris)Mutation(s): 0 
EC: 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 3.4.22.29 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q66578 (Human parechovirus 1 (strain Harris))
Explore Q66578 
Go to UniProtKB:  Q66578
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
capsid subunit VP0C289Echovirus 22 (strain Harris)Mutation(s): 0 
EC: 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 3.4.22.29 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q66578 (Human parechovirus 1 (strain Harris))
Explore Q66578 
Go to UniProtKB:  Q66578
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')D6Echovirus 22 (strain Harris)
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.10 Å
    • R-Value Work: 0.290 
    • Space Group: P 63 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 399.5α = 90
    b = 399.5β = 90
    c = 332.86γ = 120
    Software Package:
    Software NamePurpose
    CNSrefinement
    XDSdata reduction
    SCALAdata scaling
    PHASERphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2015-11-18
      Type: Initial release
    • Version 1.1: 2015-12-02
      Changes: Database references
    • Version 1.2: 2016-01-27
      Changes: Database references
    • Version 1.3: 2019-02-20
      Changes: Advisory, Data collection, Derived calculations