7TAJ | pdb_00007taj

Cryo-EM structure of Human Enterovirus D68 US/MO/14-18947 strain in complex with inhibitor 11526093 (no/low occupancy-no inhibitor modeled)

• PDB DOI: https://doi.org/10.2210/pdb7TAJ/pdb
• EM Map EMD-25776: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): enterovirus D68
• Mutation(s): No 


• Deposited: 2021-12-20 Released: 2023-01-25 
• Deposition Author(s): Fu, J., Klose, T., Kuhn, R.J., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Efficacy of an isoxazole-3-carboxamide analog of pleconaril in mouse models of Enterovirus-D68 and Coxsackie B5.

Lane, T.R., Fu, J., Sherry, B., Tarbet, B., Hurst, B.L., Riabova, O., Kazakova, E., Egorova, A., Clarke, P., Leser, J.S., Frost, J., Rudy, M., Tyler, K.L., Klose, T., Volobueva, A.S., Belyaevskaya, S.V., Zarubaev, V.V., Kuhn, R.J., Makarov, V., Ekins, S.

(2023) Antiviral Res 216: 105654-105654

• PubMed: 37327878 
• DOI: https://doi.org/10.1016/j.antiviral.2023.105654
• Primary Citation Related Structures: 
  7T9P, 7TAF, 7TAG, 7TAH, 7TAJ


• PubMed Abstract: 
  

  Enteroviruses (EV) cause a number of life-threatening infectious diseases. EV-D68 is known to cause respiratory illness in children that can lead to acute flaccid myelitis. Coxsackievirus B5 (CVB5) is commonly associated with hand-foot-mouth disease. There is no antiviral treatment available for either. We have developed an isoxazole-3-carboxamide analog of pleconaril (11526092) which displayed potent inhibition of EV-D68 (IC ₅₀ 58 nM) as well as other enteroviruses including the pleconaril-resistant Coxsackievirus B3-Woodruff (IC ₅₀ 6-20 nM) and CVB5 (EC ₅₀ 1 nM). Cryo-electron microscopy structures of EV-D68 in complex with 11526092 and pleconaril demonstrate destabilization of the EV-D68 MO strain VP1 loop, and a strain-dependent effect. A mouse respiratory model of EV-D68 infection, showed 3-log decreased viremia, favorable cytokine response, as well as statistically significant 1-log reduction in lung titer reduction at day 5 after treatment with 11526092. An acute flaccid myelitis neurological infection model did not show efficacy. 11526092 was tested in a mouse model of CVB5 infection and showed a 4-log TCID ₅₀ reduction in the pancreas. In summary, 11526092 represents a potent in vitro inhibitor of EV with in vivo efficacy in EV-D68 and CVB5 animal models suggesting it is worthy of further evaluation as a potential broad-spectrum antiviral therapeutic against EV.

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Organizational Affiliation: 
• Collaborations Pharmaceuticals Inc., Raleigh, NC, USA.
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Department of Molecular Biomedical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.
Institute for Antiviral Research, Utah State University, Logan, UT, USA; Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.
Research Center of Biotechnology RAS, 33-1 Leninsky prospect, 119071, Moscow, Russia.
Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Department of Immunology and Microbiology, Infectious Disease, Medicine and Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Department of Veterans Affairs, Aurora, CO, USA.
Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Veterans Affairs, Aurora, CO, USA.
Saint Petersburg Pasteur Institute, 14 Mira Street, 197101, Saint Petersburg, Russia.
Collaborations Pharmaceuticals Inc., Raleigh, NC, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 93.84 kDa 
• Atom Count: 6,375 
• Modeled Residue Count: 820 
• Deposited Residue Count: 849 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 1	A	296	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68) Explore A0A097BW12  Go to UniProtKB:  A0A097BW12

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 3	B [auth C]	247	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68) Explore A0A097BW12  Go to UniProtKB:  A0A097BW12

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 2	C [auth B]	238	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68) Explore A0A097BW12  Go to UniProtKB:  A0A097BW12

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
viral protein 4	D	68	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68) Explore A0A097BW12  Go to UniProtKB:  A0A097BW12

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Fu, J., Klose, T., Kuhn, R.J., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI011219

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Data collection, Refinement description
• Version 1.2: 2026-03-25
  Changes: Data collection, Database references, Structure summary