9FHP | pdb_00009fhp

CryoEM structure of wild-type Turnip Yellows Virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structure of the turnip yellows virus particles.

Lai-Kee-Him, J.Trapani, S.Boissinot, S.Reinbold, C.Fallet, C.Ancelin, A.Lecorre, F.Hoh, F.Ziegler-Graff, V.Brault, V.Bron, P.

(2025) Virology 607: 110514-110514

  • DOI: https://doi.org/10.1016/j.virol.2025.110514
  • Primary Citation of Related Structures:  
    9FHP, 9Q8J

  • PubMed Abstract: 

    Turnip yellows virus (TuYV) is a plant virus infecting important crops such as oilseed rape. TuYV is phloem-restricted and transmitted by aphids. The capsid contains two subunit types: the major capsid protein (CP) and a minor component (RTP∗) which arises from the C-terminal cleavage of a readthrough product (RTP). RTP∗ contains the CP sequence fused with a structured domain, denoted N RTD, which is a key determinant of virus transmission. Though both CP and RTP∗ are involved in virus movement and aphid transmission, how RTP∗ is incorporated into the capsid is poorly understood. We present here the structural characterisation, by immunogold labelling and 3D cryo-EM, of the wild-type TuYV and a mutant whose capsid contains the CP only. We show that incorporation of RTP∗ does not impair the capsid structure, and the N RTD does not adopt well-defined positions at the capsid surface. The number of incorporated RTP∗s suggests a random insertion.


  • Organizational Affiliation
    • Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France. Electronic address: josephine.laikeehim@cbs.cnrs.fr.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Minor capsid readthrough protein
A, B, C
202Turnip yellows virusMutation(s): 0 
Gene Names: ORF3/ORF5
UniProt
Find proteins for P09514 (Turnip yellows virus (isolate FL-1))
Explore P09514 
Go to UniProtKB:  P09514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09514
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 2.0: 2025-02-12
    Type: Coordinate replacement
    Reason: Polymer geometry
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2025-05-21
    Changes: Database references