8OPD

Virus-like Particle based on PVY coat protein with dC40 deletion with stacked-ring architecture


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y.

Kavcic, L.Kezar, A.Koritnik, N.Znidaric, M.T.Klobucar, T.Vicic, Z.Merzel, F.Holden, E.Benesch, J.L.P.Podobnik, M.

(2024) Commun Chem 7: 14-14

  • DOI: https://doi.org/10.1038/s42004-024-01100-x
  • Primary Citation of Related Structures:  
    8OPA, 8OPB, 8OPC, 8OPD, 8OPE, 8OPF, 8OPG, 8OPH, 8OPJ, 8OPK, 8OPL

  • PubMed Abstract: 

    The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.


  • Organizational Affiliation

    Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein (Fragment)227Potato virus Y strain NTNMutation(s): 0 
UniProt
Find proteins for A0A0A7DJG2 (Potato virus Y)
Explore A0A0A7DJG2 
Go to UniProtKB:  A0A0A7DJG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7DJG2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20
RECONSTRUCTIONRELION
RECONSTRUCTIONPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0391
Slovenian Research AgencySloveniaJ7-7248
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015043

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references