7ANM

Nudaurelia capensis omega virus capsid: virus-like particles expressed in Nicotiana benthamiana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus.

Castells-Graells, R.Ribeiro, J.R.S.Domitrovic, T.Hesketh, E.L.Scarff, C.A.Johnson, J.E.Ranson, N.A.Lawson, D.M.Lomonossoff, G.P.

(2021) Commun Biol 4: 619-619

  • DOI: https://doi.org/10.1038/s42003-021-02134-w
  • Primary Citation of Related Structures:  
    7ANM, 7ATA

  • PubMed Abstract: 

    Many virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus maturation, we transiently expressed the capsid protein of the insect virus Nudaurelia capensis omega virus (NωV) in Nicotiana benthamiana and were able to purify both immature procapsids and mature capsids from infiltrated leaves by varying the expression time. Cryo-EM analysis of the plant-produced procapsids and mature capsids to 6.6 Å and 2.7 Å resolution, respectively, reveals that in addition to large scale rigid body motions, internal regions of the subunits are extensively remodelled during maturation, creating the active site required for autocatalytic cleavage and infectivity. The mature particles are biologically active in terms of their ability to lyse membranes and have a structure that is essentially identical to authentic virus. The ability to faithfully recapitulate and visualize a complex maturation process in plants, including the autocatalytic cleavage of the capsid protein, has revealed a ~30 Å translation-rotation of the subunits during maturation as well as conformational rearrangements in the N and C-terminal helical regions of each subunit.


  • Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Colney, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
p70A,
C [auth B],
E [auth C],
G [auth D]
570Nudaurelia capensis omega virusMutation(s): 2 
UniProt
Find proteins for Q4TVS9 (Nudaurelia capensis omega virus)
Explore Q4TVS9 
Go to UniProtKB:  Q4TVS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4TVS9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
p70B [auth aa],
D [auth bb],
F [auth cc],
H [auth dd]
74Nudaurelia capensis omega virusMutation(s): 1 
UniProt
Find proteins for Q4TVS9 (Nudaurelia capensis omega virus)
Explore Q4TVS9 
Go to UniProtKB:  Q4TVS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4TVS9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBBS/E/J/000PR9794
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L014130/1
John Innes FoundationUnited KingdomNone

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Derived calculations, Refinement description