9FHP | pdb_00009fhp

CryoEM structure of wild-type Turnip Yellows Virus

• PDB DOI: https://doi.org/10.2210/pdb9FHP/pdb
• EM Map EMD-10003: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Turnip yellows virus
• Expression System: Nicotiana benthamiana
• Mutation(s): No 


• Deposited: 2024-05-28 Released: 2024-06-05 
• Deposition Author(s): Trapani, S., Lai Kee Him, J., Hoh, F., Brault, V., Bron, P.
• Funding Organization(s): French Infrastructure for Integrated Structural Biology (FRISBI)

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 40179450 
• DOI: https://doi.org/10.1016/j.virol.2025.110514
• Primary Citation 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.

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Organizational Affiliation: 
• Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France. Electronic address: [e-mail].
Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France. Electronic address: [e-mail].
INRAE, Université de Strasbourg, UMR SVQV, Colmar, France. Electronic address: [e-mail].
INRAE, Université de Strasbourg, UMR SVQV, Colmar, France. Electronic address: [e-mail].
Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France.
Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France. Electronic address: [e-mail].
Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France. Electronic address: [e-mail].
Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France. Electronic address: [e-mail].
Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France. Electronic address: [e-mail].
INRAE, Université de Strasbourg, UMR SVQV, Colmar, France. Electronic address: [e-mail].
Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, Montpellier, France. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 67.57 kDa 
• Atom Count: 3,208 
• Modeled Residue Count: 419 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid readthrough protein	A, B, C	202	Turnip yellows virus	Mutation(s): 0  Gene Names: ORF3/ORF5
UniProt
Find proteins for P09514 (Turnip yellows virus (isolate FL-1)) Explore P09514  Go to UniProtKB:  P09514

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Trapani, S., Lai Kee Him, J., Hoh, F., Brault, V., Bron, P.

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Funding Organization	Location	Grant Number
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INSB-05

Revision History  

• 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