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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 sho ...

    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

    Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, 00790, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAPSID SUBUNIT VP1
A
234Human parechovirus 1 (strain Harris)EC: 3.6.1.15, 3.4.22.28, 2.7.7.48
Find proteins for Q66578 (Human parechovirus 1 (strain Harris))
Go to UniProtKB:  Q66578
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CAPSID SUBUNIT VP3
B
253Human parechovirus 1 (strain Harris)EC: 3.6.1.15, 3.4.22.28, 2.7.7.48
Find proteins for Q66578 (Human parechovirus 1 (strain Harris))
Go to UniProtKB:  Q66578
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CAPSID SUBUNIT VP0
C
289Human parechovirus 1 (strain Harris)EC: 3.6.1.15, 3.4.22.28, 2.7.7.48
Find proteins for Q66578 (Human parechovirus 1 (strain Harris))
Go to UniProtKB:  Q66578
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')D6Echovirus 22 (strain Harris)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.258 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 399.500α = 90.00
b = 399.500β = 90.00
c = 332.860γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CNSrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant 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
Royal Society Leverhulme Trust Senior Research FellowshipUnited KingdomLT130088
Leverhulme Trust Research FellowshipUnited KingdomECF2013-019

Revision History 

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