9Q8J | pdb_00009q8j

CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain

• PDB DOI: https://doi.org/10.2210/pdb9Q8J/pdb
• Entry: 9Q8J supersedes: 6RTK
• EM Map EMD-10001: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Turnip yellows virus
• Expression System: Claytonia perfoliata
• Mutation(s): No 


• Deposited: 2025-02-24 Released: 2025-05-07 
• 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)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 of Related Structures:  
  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: [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 
• Modelled 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: 3.47 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: 2025-05-07 
Deposition Author(s): Trapani, S., Lai Kee Him, J., Hoh, F., Brault, V., Bron, P.
• This entry supersedes: 6RTK

---

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

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release