6M03

The crystal structure of COVID-19 main protease in apo form

• PDB DOI:  https://doi.org/10.2210/pdb6M03/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-19 Released: 2020-03-11 
• Deposition Author(s): Zhang, B., Zhao, Y., Jin, Z., Liu, X., Yang, H., Rao, Z.
• Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.201 

Literature

Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.

Zhao, Y., Zhu, Y., Liu, X., Jin, Z., Duan, Y., Zhang, Q., Wu, C., Feng, L., Du, X., Zhao, J., Shao, M., Zhang, B., Yang, X., Wu, L., Ji, X., Guddat, L.W., Yang, K., Rao, Z., Yang, H.

(2022) Proc Natl Acad Sci U S A 119: e2117142119-e2117142119

• PubMed: 35380892 
• DOI: https://doi.org/10.1073/pnas.2117142119
• Primary Citation of Related Structures:  
  6M03, 7DVP, 7DVW, 7DVX, 7DVY, 7DW0, 7DW6, 7E5X, 7VAH


• PubMed Abstract: 
  

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key enzyme, which extensively digests CoV replicase polyproteins essential for viral replication and transcription, making it an attractive target for antiviral drug development. However, the molecular mechanism of how Mpro of SARS-CoV-2 digests replicase polyproteins, releasing the nonstructural proteins (nsps), and its substrate specificity remain largely unknown. Here, we determine the high-resolution structures of SARS-CoV-2 Mpro in its resting state, precleavage state, and postcleavage state, constituting a full cycle of substrate cleavage. The structures show the delicate conformational changes that occur during polyprotein processing. Further, we solve the structures of the SARS-CoV-2 Mpro mutant (H41A) in complex with six native cleavage substrates from replicase polyproteins, and demonstrate that SARS-CoV-2 Mpro can recognize sequences as long as 10 residues but only have special selectivity for four subsites. These structural data provide a basis to develop potent new inhibitors against SARS-CoV-2.

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Organizational Affiliation: 

Shanghai Clinical Research and Trial Center, Shanghai 201210, China.

Biological Assembly 1  

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: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 33.83 kDa 
• Atom Count: 2,454 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

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: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.964	α = 90
b = 53.45	β = 101.83
c = 45.029	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Zhang, B., Zhao, Y., Jin, Z., Liu, X., Yang, H., Rao, Z.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	2017YFC0840300
National Natural Science Foundation of China (NSFC)	China	81520108019

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2020-06-10
  Changes: Database references, Structure summary
• Version 1.3: 2021-03-10
  Changes: Structure summary
• Version 1.4: 2022-09-14
  Changes: Database references