8XDL | pdb_00008xdl

F-actin-END

• PDB DOI: https://doi.org/10.2210/pdb8XDL/pdb
• EM Map EMD-38280: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2023-12-11 Released: 2024-12-18 
• Deposition Author(s): Wang, L., Li, J., Liu, T., Huang, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.44 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Aglycone Polyether Ionophores Affecting Actin Filaments as Broad-Spectrum Antiviral Agents.

Huang, M., Li, J., Li, J., Hu, B., Liu, R., Huang, L., Wang, C., Hua, R., Wu, C., Li, Z., Zhang, Z., Zhang, Y., Wu, Y., Zhang, Q., Wang, Y., Liu, J., Deng, Z., Wang, W., Hou, W., Zhao, L., Xia, Y., Zhang, X., Wang, L., Zhang, B., Liu, T.

(2025) Acs Pharmacol Transl Sci 8: 2018-2032

• PubMed: 40672661 
• DOI: https://doi.org/10.1021/acsptsci.5c00144
• Primary Citation Related Structures: 
  8XDL, 8XDM


• PubMed Abstract: 
  

  RNA viruses have high mutation rates and constitute an increasing global risk. As the viral target approach to develop antiviral drugs is inadequate for responding to an increasing diversity of viruses, an urgent need exists for the development of new antivirals to prevent future outbreaks. Here, we show that aglycone ionophores maduramycin (Mad) and endusamycin (End) from Streptomyces are broadly virucidal against cytoplasmic replicated viruses, including Japanese encephalitis virus (JEV), rabies virus, hepatitis C virus, vesicular stomatitis virus, hantavirus, dengue virus, Zika virus, chikungunya virus, and SARS-CoV-2 in vitro. Mechanistic studies suggest Mad and End can target actin filaments and displace the DNase-I-binding loop (D-loop) into an outward conformation for stabilizing actin filaments and primarily inhibit viral replication. Liposome-encapsulated Mad or End fully protects mice against JEV infection in vivo. Thus, our results may provide potential and naturally produced antivirals to prevent the spread of viruses in animals.

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Organizational Affiliation: 
• Wuhan Hesheng Tech Co., Ltd., Wuhan, 430075, China.
Department Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430000, China.
Hubei Jiangxia Laboratory, Wuhan, Hubei 430200, China.
Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences Wuhan University, Wuhan 430000, China.
Precision Cancer Diagnostic Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, China.
Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 127.68 kDa 
• Atom Count: 8,746 
• Modeled Residue Count: 1,109 
• Deposited Residue Count: 1,131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, B, C	377	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A, B, C	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.44 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Wang, L., Li, J., Liu, T., Huang, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection
• Version 1.2: 2025-12-31
  Changes: Data collection, Database references