7V7M | pdb_00007v7m

crystal structure of SARS-CoV-2 3CL protease

• PDB DOI: https://doi.org/10.2210/pdb7V7M/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-21 Released: 2022-06-29 
• Deposition Author(s): Yi, Y., Zhang, M., Ye, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.292 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Schaftoside inhibits 3CL pro and PL pro of SARS-CoV-2 virus and regulates immune response and inflammation of host cells for the treatment of COVID-19.

Yi, Y., Zhang, M., Xue, H., Yu, R., Bao, Y.O., Kuang, Y., Chai, Y., Ma, W., Wang, J., Shi, X., Li, W., Hong, W., Li, J., Muturi, E., Wei, H., Wlodarz, J., Roszak, S., Qiao, X., Yang, H., Ye, M.

(2022) Acta Pharm Sin B 12: 4154-4164

• PubMed: 35968270 
• DOI: https://doi.org/10.1016/j.apsb.2022.07.017
• Primary Citation Related Structures: 
  7V7M


• PubMed Abstract: 
  

  It is an urgent demand worldwide to control the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The 3-chymotrypsin-like protease (3CL ^pro ) and papain-like protease (PL ^pro ) are key targets to discover SARS-CoV-2 inhibitors. After screening 12 Chinese herbal medicines and 125 compounds from licorice, we found that a popular natural product schaftoside inhibited 3CL ^pro and PL ^pro with IC ₅₀ values of 1.73 ± 0.22 and 3.91 ± 0.19 μmol/L, respectively, and inhibited SARS-CoV-2 virus in Vero E6 cells with EC ₅₀ of 11.83 ± 3.23 μmol/L. Hydrogen-deuterium exchange mass spectrometry analysis, quantum mechanics/molecular mechanics calculations, together with site-directed mutagenesis indicated the antiviral activities of schaftoside were related with non-covalent interactions with H41, G143 and R188 of 3CL ^pro , and K157, E167 and A246 of PL ^pro . Moreover, proteomics analysis and cytokine assay revealed that schaftoside also regulated immune response and inflammation of the host cells. The anti-inflammatory activities of schaftoside were confirmed on lipopolysaccharide-induced acute lung injury mice. Schaftoside showed good safety and pharmacokinetic property, and could be a promising drug candidate for the prevention and treatment of COVID-19.

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Organizational Affiliation: 
• State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Faculty of Science and Technology, University of Silesia, Katowice 40-007, Poland.
Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland.

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: 33.83 kDa 
• Atom Count: 2,400 
• Modeled Residue Count: 299 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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: 2.08 Å
• R-Value Free:  0.292 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.657	α = 90
b = 53.475	β = 101.18
c = 113.534	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Yi, Y., Zhang, M., Ye, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-01-17
  Changes: Database references