7N5Z

SARS-CoV-2 Main protease C145S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.

Noske, G.D.Nakamura, A.M.Gawriljuk, V.O.Fernandes, R.S.Lima, G.M.A.Rosa, H.V.D.Pereira, H.D.Zeri, A.C.M.Nascimento, A.F.Z.Freire, M.C.L.C.Fearon, D.Douangamath, A.von Delft, F.Oliva, G.Godoy, A.S.

(2021) J Mol Biol 433: 167118-167118

  • DOI: 10.1016/j.jmb.2021.167118
  • Primary Citation of Related Structures:  
    7KFI, 7KPH, 7KVL, 7KVR, 7LDX, 7LFE, 7LFP, 7MBG, 7N5Z, 7N6N

  • PubMed Abstract: 
  • SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral M pro is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. The lack of structural information for intermediary forms of M pro is a setback for the understanding its self-maturation process ...

    SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral M pro is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. The lack of structural information for intermediary forms of M pro is a setback for the understanding its self-maturation process. Herein, we used X-ray crystallography combined with biochemical data to characterize multiple forms of SARS-CoV-2 M pro . For the immature form, we show that extra N-terminal residues caused conformational changes in the positioning of domain-three over the active site, hampering the dimerization and diminishing its activity. We propose that this form preludes the cis and trans-cleavage of N-terminal residues. Using fragment screening, we probe new cavities in this form which can be used to guide therapeutic development. Furthermore, we characterized a serine site-directed mutant of the M pro bound to its endogenous N and C-terminal residues during dimeric association stage of the maturation process. We suggest this form is a transitional state during the C-terminal trans-cleavage. This data sheds light in the structural modifications of the SARS-CoV-2 main protease during its self-maturation process.


    Organizational Affiliation

    Institute of Physics of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil. Electronic address: andregodoy@ifsc.usp.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.861α = 90
b = 53.403β = 101.86
c = 44.779γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report




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: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2021-07-28
    Changes: Database references