8KIA | pdb_00008kia

Tomato spotted wilt virus L protein (apo state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41477-025-01940-y
  • Primary Citation of 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.


  • Organizational Affiliation
    • State Key Laboratory of Agricultural and Forestry Biosecurity, Nanjing Agricultural University, Nanjing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L1,776Orthotospovirus tomatomaculaeMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for A0A7G8JUR3 (Tomato spotted wilt virus)
Explore A0A7G8JUR3 
Go to UniProtKB:  A0A7G8JUR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7G8JUR3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • 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