SARS-CoV-2 Main Protease (Mpro) H163A Mutant Reduced with 20mM TCEP

Experimental Data Snapshot

  • Resolution: 2.49 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease.

Tran, N.Dasari, S.Barwell, S.A.E.McLeod, M.J.Kalyaanamoorthy, S.Holyoak, T.Ganesan, A.

(2023) Nat Commun 14: 5625-5625

  • DOI: https://doi.org/10.1038/s41467-023-40023-4
  • Primary Citation of Related Structures:  
    8DD6, 8DDL, 8SG6

  • PubMed Abstract: 

    The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium.

  • Organizational Affiliation

    Physics Department, Cornell University, Ithaca, NY, 14853, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
EC: (PDB Primary Data), (UniProt), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), (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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.49 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.873α = 90
b = 103.413β = 90
c = 103.694γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release