5MJV

Rebuild and re-refined model for Human Parechovirus 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Genomic RNA folding mediates assembly of human parechovirus.

Shakeel, S.Dykeman, E.C.White, S.J.Ora, A.Cockburn, J.J.Butcher, S.J.Stockley, P.G.Twarock, R.

(2017) Nat Commun 8: 5-5

  • DOI: 10.1038/s41467-016-0011-z
  • Primary Citation of Related Structures:  
    5MJV

  • PubMed Abstract: 
  • Assembly of the major viral pathogens of the Picornaviridae family is poorly understood. Human parechovirus 1 is an example of such viruses that contains 60 short regions of ordered RNA density making identical contacts with the protein shell. We show here via a combination of RNA-based systematic evolution of ligands by exponential enrichment, bioinformatics analysis and reverse genetics that these RNA segments are bound to the coat proteins in a sequence-specific manner ...

    Assembly of the major viral pathogens of the Picornaviridae family is poorly understood. Human parechovirus 1 is an example of such viruses that contains 60 short regions of ordered RNA density making identical contacts with the protein shell. We show here via a combination of RNA-based systematic evolution of ligands by exponential enrichment, bioinformatics analysis and reverse genetics that these RNA segments are bound to the coat proteins in a sequence-specific manner. Disruption of either the RNA coat protein recognition motif or its contact amino acid residues is deleterious for viral assembly. The data are consistent with RNA packaging signals playing essential roles in virion assembly. Their binding sites on the coat proteins are evolutionarily conserved across the Parechovirus genus, suggesting that they represent potential broad-spectrum anti-viral targets.The mechanism underlying packaging of genomic RNA into viral particles is not well understood for human parechoviruses. Here the authors identify short RNA motifs in the parechovirus genome that bind capsid proteins, providing approximately 60 specific interactions for virion assembly.


    Organizational Affiliation

    Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK. reidun.twarock@york.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAPSID SUBUNIT VP1A234Echovirus 22 (strain Harris)Mutation(s): 0 
EC: 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.4.22.29 (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 proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CAPSID SUBUNIT VP3B253Echovirus 22 (strain Harris)Mutation(s): 0 
EC: 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.4.22.29 (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 proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CAPSID SUBUNIT VP0C289Echovirus 22 (strain Harris)Mutation(s): 0 
EC: 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.4.22.29 (UniProt)
UniProt
Find proteins for Q66578 (Human parechovirus 1 (strain Harris))
Explore Q66578 
Go to UniProtKB:  Q66578
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*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: 3.09 Å
    • R-Value Free: 0.261 
    • R-Value Work: 0.258 
    • R-Value Observed: 0.258 
    • 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
    XDSdata reduction
    SCALAdata scaling
    PHASERphasing
    CNSrefinement
    REFMACrefinement

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Academy of FinlandFinland139178
    Academy of FinandFinland275199
    Sigrid Juselius FoundationFinland--
    Wellcome TrustUnited Kingdom062164
    Wellcome TrustUnited Kingdom090932/Z/09/Z
    Wellcome TrustUnited Kingdom097827/Z/11/Z
    Leverhulme TrustUnited KingdomLT130088
    Leverhulme Trust Research FellowshipUnited KingdomECF2013-019

    Revision History  (Full details and data files)

    • Version 1.0: 2017-01-11
      Type: Initial release
    • Version 1.1: 2017-03-08
      Changes: Database references
    • Version 1.2: 2017-08-30
      Changes: Author supporting evidence
    • Version 1.3: 2018-01-31
      Changes: Author supporting evidence