5MUU

dsRNA bacteriophage phi6 nucleocapsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/ncomms14814
  • Primary Citation of Related Structures:  
    5MUU, 5MUV, 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. 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.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major inner protein P1
A, B
769Cystovirus phi6Mutation(s): 0 
UniProt
Find proteins for P11126 (Pseudomonas phage phi6)
Explore P11126 
Go to UniProtKB:  P11126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11126
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Packaging enzyme P4332Cystovirus phi6Mutation(s): 0 
EC: 3.6.1.15
UniProt
Find proteins for P11125 (Pseudomonas phage phi6)
Explore P11125 
Go to UniProtKB:  P11125
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11125
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Major outer capsid protein
D, E, F, G, H
D, E, F, G, H, I, J, K, L, M
149Cystovirus phi6Mutation(s): 0 
UniProt
Find proteins for P07579 (Pseudomonas phage phi6)
Explore P07579 
Go to UniProtKB:  P07579
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07579
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTCoot0.8.7
MODEL REFINEMENTPHENIX1.10.1_2155
MODEL REFINEMENTCoot0.8.7
MODEL REFINEMENTPHENIX1.10.1_2155
MODEL REFINEMENTCoot0.8.7
MODEL REFINEMENTPHENIX1.10.1_2155

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-10-23
    Changes: Data collection, Other