8EYJ

Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S mutant in complex with Nirmatrelvir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition.

Noske, G.D.Song, Y.Fernandes, R.S.Chalk, R.Elmassoudi, H.Koekemoer, L.Owen, C.D.El-Baba, T.J.Robinson, C.V.Oliva, G.Godoy, A.S.

(2023) Nat Commun 14: 1545-1545

  • DOI: https://doi.org/10.1038/s41467-023-37035-5
  • Primary Citation of Related Structures:  
    8EY2, 8EYJ

  • PubMed Abstract: 

    The main protease from SARS-CoV-2 (M pro ) is responsible for cleavage of the viral polyprotein. M pro self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S M pro to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of M pro N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the M pro dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.


  • Organizational Affiliation

    Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
307Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4WI (Subject of Investigation/LOI)
Query on 4WI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
C23 H34 F3 N5 O4
WDVIRQQKRMIXGS-XIFHJVQQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.646α = 90
b = 101.969β = 90
c = 103.626γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4WIClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Database references
  • Version 1.3: 2023-07-26
    Changes: Data collection
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary