5MUV

Atomic structure fitted into a localized reconstruction of bacteriophage phi6 packaging hexamer P4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Double-stranded RNA virus outer shell assembly by bona fide domain-swapping.

Sun, Z.El Omari, K.Sun, X.Ilca, S.L.Kotecha, A.Stuart, D.I.Poranen, M.M.Huiskonen, J.T.

(2017) Nat Commun 8: 14814-14814

  • DOI: 10.1038/ncomms14814
  • Primary Citation of Related Structures:  
    5MUV, 5MUU, 5MUW

  • PubMed Abstract: 
  • Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle ...

    Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution.


    Related Citations: 
    • Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.
      El Omari, K., Meier, C., Kainov, D., Sutton, G., Grimes, J.M., Poranen, M.M., Bamford, D.H., Tuma, R., Stuart, D.I., Mancini, E.J.
      (2013) Nucleic Acids Res 41: 9396

    Organizational Affiliation

    Department of Biosciences, University of Helsinki, Viikinkaari 9, Helsinki 00014, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Packaging enzyme P4A, B, C [auth I], D [auth J], E [auth K], F [auth L]309Pseudomonas virus phi6Mutation(s): 0 
Gene Names: P4
EC: 3.6.1.15
UniProt
Find proteins for P11125 (Pseudomonas phage phi6)
Explore P11125 
Go to UniProtKB:  P11125
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Finland--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 2.0: 2017-08-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Refinement description
  • Version 2.1: 2018-01-31
    Changes: Advisory, Data processing, Other
  • Version 3.0: 2019-04-24
    Changes: Atomic model, Data collection, Derived calculations, Other