8KI7 | pdb_00008ki7

Structure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'vRNA

• PDB DOI: https://doi.org/10.2210/pdb8KI7/pdb
• EM Map EMD-37253: EMDB EMDataResource
• NAKB: 8KI7

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Tomato spotted wilt virus (strain Bulgarian L3), synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-08-23 Released: 2024-09-25 
• Deposition Author(s): Cao, L., Wang, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for the activation of plant bunyavirus replication machinery and its dual-targeted inhibition by ribavirin.

Li, J., Cao, L., Zhao, Y., Shen, J., Wang, L., Feng, M., Zhu, M., Ye, Y., Kormelink, R., Tao, X., Wang, X.

(2025) Nat Plants 11: 518-530

• PubMed: 40044941 
• DOI: https://doi.org/10.1038/s41477-025-01940-y
• Primary Citation Related Structures: 
  8KI6, 8KI7, 8KI8, 8KI9, 8KIA, 9J8V


• PubMed Abstract: 
  

  Despite the discovery of plant viruses as a new class of pathogens over a century ago, the structure of plant virus replication machinery and antiviral pesticide remains lacking. Here we report five cryogenic electron microscopy structures of a ~330-kDa RNA-dependent RNA polymerase (RdRp) from a devastating plant bunyavirus, tomato spotted wilt orthotospovirus (TSWV), including the apo, viral-RNA-bound, base analogue ribavirin-bound and ribavirin-triphosphate-bound states. They reveal that a flexible loop of RdRp's motif F functions as 'sensor' to perceive viral RNA and further acts as an 'adaptor' to promote the formation of a complete catalytic centre. A ten-base RNA 'hook' structure is sufficient to trigger major conformational changes and activate RdRp. Chemical screening showed that ribavirin is effective against TSWV, and structural data revealed that ribavirin disrupts both hook-binding and catalytic core formation, locking polymerase in its inactive state. This work provides structural insights into the mechanisms of plant bunyavirus RdRp activation and its dual-targeted site inhibition, facilitating the development of pesticides against plant viruses.

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Organizational Affiliation: 
• State Key Laboratory of Agricultural and Forestry Biosecurity, Nanjing Agricultural University, Nanjing, China.
Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China.
State and Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, China.
CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Laboratory of Virology, Department of Plant Sciences, Wageningen University, Wageningen, the Netherlands.
State Key Laboratory of Agricultural and Forestry Biosecurity, Nanjing Agricultural University, Nanjing, China. [e-mail].
Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China. [e-mail].
State and Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, China. [e-mail].
CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 250.54 kDa 
• Atom Count: 16,784 
• Modeled Residue Count: 2,035 
• Deposited Residue Count: 2,122 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	2,090	Tomato spotted wilt virus (strain Bulgarian L3)	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for A0A7G8JUQ8 (Tomato spotted wilt virus) Explore A0A7G8JUQ8  Go to UniProtKB:  A0A7G8JUQ8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*GP*AP*GP*CP*AP*AP*UP*CP*A)-3')	B [auth E]	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*CP*AP*AP*UP*CP*AP*GP*G)-3')	C [auth B]	9	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*CP*CP*UP*GP*AP*UP*UP*GP*CP*UP*CP*U)-3')	D [auth F]	13	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Cao, L., Wang, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection