9QY3 | pdb_00009qy3

Structure of the Plum Pox Virus (PPV)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural characterization of plum pox virus by cryo-electron microscopy.

Bonnet, D.M.V.J.Chaves-Sanjuan, A.Contaldo, N.De Stradis, A.Caliandro, R.Minafra, A.Geuna, F.

(2025) Arch Virol 171: 11-11

  • DOI: https://doi.org/10.1007/s00705-025-06473-5
  • Primary Citation of Related Structures:  
    9QY3

  • PubMed Abstract: 

    Plum pox virus (PPV), a significant member of the genus Potyvirus, represents a global agricultural challenge, causing significant economic losses and threatening fruit farming due to its easy transmission to most Prunus species. Here, we present the high-resolution structural characterization of PPV using cryo-electron microscopy (cryo-EM). The reconstructed structure at 2.9 Å reveals a filamentous virion with a helical assembly formed by the coat protein (CP), which encapsidates a single-stranded RNA (ssRNA) genome. The structure of the CP core shows remarkable conservation with other potyviruses, with an RNA binding site and inter-subunit interactions mediated in part by the N-terminal arm, which is confirmed here to have a disordered structure. Mass spectrometry analysis identified numerous post-translational modifications, mostly phosphorylation, primarily in the flexible N-terminal region. In silico predictions revealed intrinsically disordered regions, which is compatible with the amyloidogenic properties of the CP. These results provide new insights into the architecture and assembly of PPV, offering a basis for future studies and, possibly, antiviral strategies.


  • Organizational Affiliation
    • Unitech NOLIMITS, Imaging Facility, Università degli Studi di Milano, Milan, Italy.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coat Protein (CP)330Plum pox virusMutation(s): 0 
UniProt
Find proteins for B6C7W4 (Plum pox virus)
Explore B6C7W4 
Go to UniProtKB:  B6C7W4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6C7W4
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNATA [auth t]624Plum pox virus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release