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 3.1 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
Packaging enzyme P4309Cystovirus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11125
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth I]
N [auth J]
P [auth K]
H [auth A],
J [auth B],
K [auth I],
N [auth J],
P [auth K],
R [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
L [auth I]
M [auth J]
O [auth K]
G [auth A],
I [auth B],
L [auth I],
M [auth J],
O [auth K],
Q [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



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
  • Version 3.1: 2024-05-15
    Changes: Data collection, Database references