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

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.201 

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This is version 1.5 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100091, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), (UniProt), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), (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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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 = 113.964α = 90
b = 53.45β = 101.83
c = 45.029γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2017YFC0840300
National Natural Science Foundation of China (NSFC)China81520108019

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-11-29
    Changes: Data collection, Refinement description