Biological Assembly 1  

 3D View: Structure

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 13-mer - A13 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 313.83 kDa 
• Atom Count: 22012 
• Modelled Residue Count: 2786 
• Deposited Residue Count: 2786 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

6R7G

Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family

• DOI: 10.2210/pdb6R7G/pdb
• EMDataResource: EMD-4740

• Classification: VIRUS
• Organism(s): Potato virus X
• Mutation(s): No 


• Deposited: 2019-03-28 Released: 2020-03-18 
• Deposition Author(s): Grinzato, A., Kandiah, E., Lico, C., Betti, C., Baschieri, S., Zanotti, G.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family.

Grinzato, A., Kandiah, E., Lico, C., Betti, C., Baschieri, S., Zanotti, G.

(2020) Nat Chem Biol 16: 564-569

• PubMed: 32203412 
• DOI: 10.1038/s41589-020-0502-4
• Primary Citation of Related Structures:  
  6R7G


• PubMed Abstract: 
  

Potato virus X (PVX) is a positive-sense single-stranded RNA (ssRNA) filamentous plant virus belonging to the Alphaflexiviridae family, considered in recent years as a tool for nanotechnology applications. We present the cryo-electron microscopy structure of the PVX particle at a resolution of 2.2 Å. The well-defined density of the coat proteins and of the genomic RNA allowed a detailed analysis of protein-RNA interactions, including those mediated by solvent molecules. The particle is formed by repeated segments made of 8.8 coat proteins, forming a left-handed helical structure. The RNA runs in an internal crevice along the virion, packaged in 5-nucleotide repeats in which the first four bases are stacked in the classical way, while the fifth is rotated and nearly perpendicular. The resolution of the structure described here suggests a mechanism for the virion assembly and potentially provides a platform for the rational design of antiviral compounds and for the use of PVX in nanotechnology.

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Organizational Affiliation: 

Department of Biomedical Sciences, University of Padua, Padua, Italy. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A,  B,  C,  D,  E,  F,  G,  H,  I,  J,  K,  L,  M	209	Potato virus X	Mutation(s): 0
Find proteins for P17782 (Potato virus X (strain X3)) Explore P17782  Go to UniProtKB:  P17782

Entity ID: 2
Molecule	Chains	Length	Organism	Image
polyU RNA	R	69	Potato virus X

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-03-28 
• Released Date: 2020-03-18 
Deposition Author(s): Grinzato, A., Kandiah, E., Lico, C., Betti, C., Baschieri, S., Zanotti, G.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Database references
• Version 1.2: 2020-05-06
  Changes: Database references