8WUR | pdb_00008wur

Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with shikonin

• PDB DOI: https://doi.org/10.2210/pdb8WUR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-10-21 Released: 2024-11-13 
• Deposition Author(s): Zhao, Z.Y., Li, W.W., Zhang, J., Li, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.238 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for the Inhibition of SARS-CoV-2 M pro D48N Mutant by Shikonin and PF-07321332.

Zhao, Z., Zhu, Q., Zhou, X., Li, W., Yin, X., Li, J.

(2023) Viruses 16

• PubMed: 38257765 
• DOI: https://doi.org/10.3390/v16010065
• Primary Citation Related Structures: 
  7XB4, 8WUR


• PubMed Abstract: 
  

  Preventing the spread of SARS-CoV-2 and its variants is crucial in the fight against COVID-19. Inhibition of the main protease (M ^pro ) of SARS-CoV-2 is the key to disrupting viral replication, making M ^pro a promising target for therapy. PF-07321332 and shikonin have been identified as effective broad-spectrum inhibitors of SARS-CoV-2 M ^pro . The crystal structures of SARS-CoV-2 M ^pro bound to PF-07321332 and shikonin have been resolved in previous studies. However, the exact mechanism regarding how SARS-CoV-2 M ^pro mutants impact their binding modes largely remains to be investigated. In this study, we expressed a SARS-CoV-2 M ^pro mutant, carrying the D48N substitution, representing a class of mutations located near the active sites of M ^pro . The crystal structures of M ^pro D48N in complex with PF-07321332 and shikonin were solved. A detailed analysis of the interactions between M ^pro D48N and two inhibitors provides key insights into the binding pattern and its structural determinants. Further, the binding patterns of the two inhibitors to M ^pro D48N mutant and wild-type M ^pro were compared in detail. This study illustrates the possible conformational changes when the M ^pro D48N mutant is bound to inhibitors. Structural insights derived from this study will inform the development of new drugs against novel coronaviruses.

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Organizational Affiliation: 
• College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.
Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China.

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: 65.86 kDa 
• Atom Count: 4,510 
• Modeled Residue Count: 586 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	296	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNO (Subject of Investigation/LOI)	C [auth A]	2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione C16 H16 O5 NEZONWMXZKDMKF-SNVBAGLBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.238 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.052	α = 90
b = 102.944	β = 90
c = 103.687	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Zhao, Z.Y., Li, W.W., Zhang, J., Li, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release