8EJ9 | pdb_00008ej9

Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates

• PDB DOI: https://doi.org/10.2210/pdb8EJ9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-09-16 Released: 2023-04-26 
• Deposition Author(s): Lu, J., Khan, M.B., Young, H.S., Lemieux, M.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.329 (Depositor), 0.331 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

Literature

SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.

Chen, S.A., Arutyunova, E., Lu, J., Khan, M.B., Rut, W., Zmudzinski, M., Shahbaz, S., Iyyathurai, J., Moussa, E.W., Turner, Z., Bai, B., Lamer, T., Nieman, J.A., Vederas, J.C., Julien, O., Drag, M., Elahi, S., Young, H.S., Lemieux, M.J.

(2023) ACS Cent Sci 9: 696-708

• PubMed: 37122453 
• DOI: https://doi.org/10.1021/acscentsci.3c00054
• Primary Citation Related Structures: 
  8DI3, 8DJJ, 8DK8, 8DKH, 8DKJ, 8DKK, 8DKL, 8DKZ, 8DMN, 8EJ7, 8EJ9


• PubMed Abstract: 
  

  The main protease of SARS-CoV-2 (M ^pro ) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in M ^pro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 M ^pro mutants provided structural insight into their altered functionality. Additionally, we show M ^pro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting M ^pro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.

---

Organizational Affiliation: 
• Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.
Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, 50-370, Poland.
Department of Dentistry & Dental Hygiene, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.
Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.
Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.
Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.81 kDa 
• Atom Count: 2,391 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.329 (Depositor), 0.331 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.62	α = 90
b = 54.5	β = 101.186
c = 44.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Lu, J., Khan, M.B., Young, H.S., Lemieux, M.J.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	VR3-172655
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	549297-2019

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-05-03
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-05-01
  Changes: Database references