6HXX | pdb_00006hxx

Potato virus Y


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 6HXX

This is version 1.2 of the entry. See complete history

Literature

Structural basis for the multitasking nature of the potato virus Y coat protein.

Kezar, A.Kavcic, L.Polak, M.Novacek, J.Gutierrez-Aguirre, I.Znidaric, M.T.Coll, A.Stare, K.Gruden, K.Ravnikar, M.Pahovnik, D.Zagar, E.Merzel, F.Anderluh, G.Podobnik, M.

(2019) Sci Adv 5: eaaw3808-eaaw3808

  • DOI: https://doi.org/10.1126/sciadv.aaw3808
  • Primary Citation Related Structures: 
    6HXX, 6HXZ

  • PubMed Abstract: 

    Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.


  • Organizational Affiliation
    • Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.

Macromolecule Content 

  • Total Structure Weight: 1,099.76 kDa 
  • Atom Count: 65,765 
  • Modeled Residue Count: 8,015 
  • Deposited Residue Count: 9,520 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coat protein267Potato virus YMutation(s): 0 
UniProt
Find proteins for A0A0A7DJ81 (Potato virus Y)
Explore A0A0A7DJ81 
Go to UniProtKB:  A0A0A7DJ81
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7DJ81
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*U)-3')5Potato virus Y
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.13.2998

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: 2019-08-07
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary