8EY2

Cryo-EM structure of SARS-CoV-2 Main protease C145S in complex with N-terminal peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7S82


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 proteinaseA,
B [auth C],
C [auth D],
D [auth B]
314Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
EC: 3.4.22.69
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: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2013/07600-3

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description