3JB4

Structure of Ljungan virus: insight into picornavirus packaging


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Ljungan virus provides insight into genome packaging of this picornavirus.

Zhu, L.Wang, X.Ren, J.Porta, C.Wenham, H.Ekstrom, J.O.Panjwani, A.Knowles, N.J.Kotecha, A.Siebert, C.A.Lindberg, A.M.Fry, E.E.Rao, Z.Tuthill, T.J.Stuart, D.I.

(2015) Nat Commun 6: 8316-8316

  • DOI: 10.1038/ncomms9316
  • Primary Citation of Related Structures:  
    3JB4

  • PubMed Abstract: 
  • Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans ...

    Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-Å resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses.


    Organizational Affiliation

    Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP1A297Ljungan virus 87-012Mutation(s): 0 
UniProt
Find proteins for Q8JV21 (Ljunganvirus 1)
Explore Q8JV21 
Go to UniProtKB:  Q8JV21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JV21
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VP0B259Ljungan virus 87-012Mutation(s): 0 
UniProt
Find proteins for Q8JV21 (Ljunganvirus 1)
Explore Q8JV21 
Go to UniProtKB:  Q8JV21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JV21
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VP3C244Ljungan virus 87-012Mutation(s): 0 
UniProt
Find proteins for Q8JV21 (Ljunganvirus 1)
Explore Q8JV21 
Go to UniProtKB:  Q8JV21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JV21
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection
  • Version 1.2: 2019-12-18
    Changes: Database references, Other