9EUR

Mpro WT from SARS-CoV-2 with 298Q mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.210 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SARS-CoV-2 M pro oligomerization as a potential target for therapy.

Lis, K.Plewka, J.Menezes, F.Bielecka, E.Chykunova, Y.Pustelny, K.Niebling, S.Garcia, A.S.Garcia-Alai, M.Popowicz, G.M.Czarna, A.Kantyka, T.Pyrc, K.

(2024) Int J Biol Macromol 267: 131392-131392

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.131392
  • Primary Citation of Related Structures:  
    9EPL, 9EPM, 9EUR, 9EUS, 9EWM, 9EWN, 9EWO

  • PubMed Abstract: 

    The main protease (M pro ) of SARS-CoV-2 is critical in the virus's replication cycle, facilitating the maturation of polyproteins into functional units. Due to its conservation across taxa, M pro is a promising target for broad-spectrum antiviral drugs. Targeting M pro with small molecule inhibitors, such as nirmatrelvir combined with ritonavir (Paxlovid™), which the FDA has approved for post-exposure treatment and prophylaxis, can effectively interrupt the replication process of the virus. A key aspect of M pro 's function is its ability to form a functional dimer. However, the mechanics of dimerization and its influence on proteolytic activity remain less understood. In this study, we utilized biochemical, structural, and molecular modelling approaches to explore M pro dimerization. We evaluated critical residues, specifically Arg4 and Arg298, that are essential for dimerization. Our results show that changes in the oligomerization state of M pro directly affect its enzymatic activity and dimerization propensity. We discovered a synergistic relationship influencing dimer formation, involving both intra- and intermolecular interactions. These findings highlight the potential for developing allosteric inhibitors targeting M pro , offering promising new directions for therapeutic strategies.


  • Organizational Affiliation

    Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland; Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24,31-155 Cracow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicase polyprotein 1a300Homo sapiensMutation(s): 0 
Gene Names: ORF1ab
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.210 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.979α = 90
b = 53.68β = 100.819
c = 113.957γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2017/27/B/NZ6/02488

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references