7MGS | pdb_00007mgs

SARS-CoV-2 main protease in complex with N-terminal autoprocessing substrate

• PDB DOI: https://doi.org/10.2210/pdb7MGS/pdb

• Classification: VIRAL PROTEIN, hydrolase
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2021-04-13 Released: 2021-06-23 
• Deposition Author(s): MacDonald, E.A., Windsor, I.W., Hinshaw, S.M.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease.

MacDonald, E.A., Frey, G., Namchuk, M.N., Harrison, S.C., Hinshaw, S.M., Windsor, I.W.

(2021) ACS Infect Dis 7: 2591-2595

• PubMed: 34437808 
• DOI: https://doi.org/10.1021/acsinfecdis.1c00237
• Primary Citation Related Structures: 
  7MGR, 7MGS


• PubMed Abstract: 
  

  The main protease (M ^pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease (COVID-19), is an ideal target for pharmaceutical inhibition. M ^pro is conserved among coronaviruses and distinct from human proteases. Viral replication depends on the cleavage of the viral polyprotein at multiple sites. We present crystal structures of SARS-CoV-2 M ^pro bound to two viral substrate peptides. The structures show how M ^pro recognizes distinct substrates and how subtle changes in substrate accommodation can drive large changes in catalytic efficiency. One peptide, constituting the junction between viral nonstructural proteins 8 and 9 (nsp8/9), has P1' and P2' residues that are unique among the SARS-CoV-2 M ^pro cleavage sites but conserved among homologous junctions in coronaviruses. M ^pro cleaves nsp8/9 inefficiently, and amino acid substitutions at P1' or P2' can enhance catalysis. Visualization of M ^pro with intact substrates provides new templates for antiviral drug design and suggests that the coronavirus lifecycle selects for finely tuned substrate-dependent catalytic parameters.

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Organizational Affiliation: 
• Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States.
Howard Hughes Medical Institute, Boston, Massachusetts 02115, United States.
Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 34.79 kDa 
• Atom Count: 2,497 
• Modeled Residue Count: 313 
• Deposited Residue Count: 315 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-ALA-VAL-LEU-GLN-SER-GLY-PHE	B	9	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.771	α = 90
b = 63.312	β = 90
c = 104.646	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): MacDonald, E.A., Windsor, I.W., Hinshaw, S.M.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2021-09-08
  Changes: Database references
• Version 1.2: 2021-09-22
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description