6HY0

Atomic models of P1, P4 C-terminal fragment and P8 fitted in the bacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus.

Ilca, S.L.Sun, X.El Omari, K.Kotecha, A.de Haas, F.DiMaio, F.Grimes, J.M.Stuart, D.I.Poranen, M.M.Huiskonen, J.T.

(2019) Nature --: --

  • DOI: 10.1038/s41586-019-1229-9

  • PubMed Abstract: 
  • Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life cycles of double-stranded (ds)DNA and dsRNA viruses a ...

    Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life cycles of double-stranded (ds)DNA and dsRNA viruses are dissimilar. In terms of nucleic acid packing, dsDNA viruses, which lack genome segmentation and intra-capsid transcriptional machinery, predominantly display single-spooled genome organizations 1-8 . Because the release of dsRNA into the cytoplasm triggers host defence mechanisms 9 , dsRNA viruses retain their genomes within a core particle that contains the enzymes required for RNA replication and transcription 10-12 . The genomes of dsRNA viruses vary greatly in the degree of segmentation. In members of the Reoviridae family, genomes consist of 10-12 segments and exhibit a non-spooled arrangement mediated by RNA-dependent RNA polymerases 11-14 . However, whether this arrangement is a general feature of dsRNA viruses remains unknown. Here, using cryo-electron microscopy to resolve the dsRNA genome structure of the tri-segmented bacteriophage ΙΈ6 of the Cystoviridae family, we show that dsRNA viruses can adopt a dsDNA-like single-spooled genome organization. We find that in this group of viruses, RNA-dependent RNA polymerases do not direct genome ordering, and the dsRNA can adopt multiple conformations. We build a model that encompasses 90% of the genome, and use this to quantify variation in the packing density and to characterize the different liquid crystalline geometries that are exhibited by the tightly compacted nucleic acid. Our results demonstrate that the canonical model for the packing of dsDNA can be extended to dsRNA viruses.


    Organizational Affiliation

    Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. juha@strubi.ox.ac.uk.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Thermo Fisher Scientific, Eindhoven, The Netherlands.,Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, UK.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland. juha@strubi.ox.ac.uk.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. juha@strubi.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major inner protein P1
A, B
769Pseudomonas phage phi6Mutation(s): 0 
Gene Names: P1
Find proteins for P11126 (Pseudomonas phage phi6)
Go to UniProtKB:  P11126
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Packaging Enzyme P4
C
332N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Major Outer Capsid Protein P8
D, E, F, G, H, I, J, K, L, M
149N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release