9JQK | pdb_00009jqk

Ebola VP30 and its inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.264 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.226 (DCC) 

Starting Model: experimental
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Literature

Ginkgolic acid inhibits Ebola virus transcription and replication by disrupting the interaction between nucleoprotein and VP30 protein.

Peng, C.Wu, F.Ma, Y.Liu, G.Huang, Y.Tong, R.Xu, W.

(2025) Antiviral Res 234: 106074-106074

  • DOI: https://doi.org/10.1016/j.antiviral.2024.106074
  • Primary Citation of Related Structures:  
    9JQK

  • PubMed Abstract: 

    The Ebola virus, a filovirus, has been responsible for significant human fatalities since its discovery. Despite extensive research, effective small-molecule drugs remain elusive due to its complex pathogenesis. Inhibition of RNA synthesis is a promising therapeutic target, and the VP30 protein plays a critical role in this process. The interaction between VP30 and the nucleoprotein (NP) is essential for viral replication. We identified ginkgolic acid as a small molecule with strong affinity for VP30, which was validated through multiple assays, including thermal shift, surface plasmon resonance, fluorescence polarization, pull-down, and co-immunoprecipitation. The antiviral efficacy of ginkgolic acid was demonstrated in the EBOV transcription- and replication-competent virus-like particle (trVLP) system. Furthermore, we resolved the crystal structure of the VP30-ginkgolic acid complex, revealing two ginkgolic acid molecules located at the VP30/NP interaction interface. This structural information provides insight into the molecular basis of ginkgolic acid's antiviral activity and suggests a novel therapeutic strategy targeting the VP30/NP interaction.


  • Organizational Affiliation
    • Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional activator VP30A [auth D],
B [auth A],
C [auth B],
D [auth C]
162Ebola virus - Zaire (1995)Mutation(s): 0 
Gene Names: VP30
UniProt
Find proteins for Q77DJ5 (Zaire ebolavirus (strain Kikwit-95))
Explore Q77DJ5 
Go to UniProtKB:  Q77DJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ77DJ5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.264 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.226 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.177α = 72.88
b = 54.042β = 85.961
c = 83.265γ = 71.779
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-04-23 
  • Deposition Author(s): Wu, F., Xu, W.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82173865

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release