Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 33.83 kDa 
• Atom Count: 2501 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

7JP1

Structure of wild-type substrate free SARS-CoV-2 Mpro.

• PDB DOI: 10.2210/pdb7JP1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-07 Released: 2020-10-07 
• Deposition Author(s): Lee, J., Worrall, L.J., Paetzel, M., Strynadka, N.C.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.

Lee, J., Worrall, L.J., Vuckovic, M., Rosell, F.I., Gentile, F., Ton, A.T., Caveney, N.A., Ban, F., Cherkasov, A., Paetzel, M., Strynadka, N.C.J.

(2020) Nat Commun 11: 5877-5877

• PubMed: 33208735 
• DOI: 10.1038/s41467-020-19662-4
• Primary Citation of Related Structures:  
  7JOY, 7JP1, 7KHP


• PubMed Abstract: 
  

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M ^pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M ^pro inhibition.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-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), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.186	α = 90
b = 52.752	β = 102.72
c = 44.575	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-08-07 
• Released Date: 2020-10-07 
Deposition Author(s): Lee, J., Worrall, L.J., Paetzel, M., Strynadka, N.C.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references