9JVU | pdb_00009jvu

Crystal structure of F10 core protein from Monkeypox virus reveals its potential inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure of F10 core protein from Mpox virus reveals its potential inhibitors.

Zhao, R.Zhu, X.Y.Zhang, J.Xie, Z.Y.Hu, W.S.Han, Q.H.Fan, J.Y.Yang, Y.N.Feng, B.Y.Cao, J.M.Zhou, X.Wang, D.P.

(2025) Int J Biol Macromol 284: 138079-138079

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.138079
  • Primary Citation of Related Structures:  
    9JVU

  • PubMed Abstract: 

    Mpox virus (MPXV), a member of Poxviridae family, causes a rare zoonotic disease. According to the most recent data, over 15,600 cases and 537 deaths of human mpox have been reported. The MPXV complete RNA polymerase (RNAP), which is responsible for the entire early transcriptional cycle, comprises the RNAP core enzyme and essential factors including viral early transcription factor (VETF), nucleoside triphosphate phosphohydrolase I (NPH-I), RNA polymerase-associated protein (Rap94), and F10 core protein. The dimeric F10 core protein stabilizes the N-terminal region of Rap94, and the C-terminal domain of NPH-I, functioning as a structural clamp that enhances the stability of the RNAP complex. Here, we determined the crystal structure of the F10 core protein at a high resolution of 1.5 Å, and identified a cavity between the F10 core protein and NPH-I through superimposition of the MPXV F10 core protein and the vaccinia virus (VACV) RNAP. We further conducted a virtual screening based on this cavity, and identified 28 compounds as potential MPXV inhibitors. To the best of our knowledge, this is the first study to screen for inhibitors targeting MPXV RNAP. Our study may facilitate the development of novel ways for the discovery of anti-MPXV compounds against emerging pathogens.


  • Organizational Affiliation
    • Department of Cardiology, the First hospital of Shanxi Medical University, and Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China; Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein OPG073132Monkeypox virusMutation(s): 0 
Gene Names: OPG073MPXVgp059
UniProt
Find proteins for A0A7H0DN46 (Monkeypox virus)
Explore A0A7H0DN46 
Go to UniProtKB:  A0A7H0DN46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DN46
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.834α = 90
b = 69.312β = 90
c = 64.829γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32401055

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Database references