The Crystal Structure of Main Protease from Mouse Hepatitis Virus A59 in Complex with an inhibitor

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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The crystal structure of main protease from mouse hepatitis virus A59 in complex with an inhibitor.

Cui, W.Cui, S.Chen, C.Chen, X.Wang, Z.Yang, H.Zhang, L.

(2019) Biochem Biophys Res Commun 511: 794-799

  • DOI: https://doi.org/10.1016/j.bbrc.2019.02.105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Mouse hepatitis virus A59 (MHV-A59) is a representative member of the genus betacoronavirus within the subfamily Coronavirinae, which infects the liver, brain and respiratory tract. Through different inoculation routes, MHV-A59 can provide animal models for encephalitis, hepatitis and pneumonia to explore viral life machinery and virus-host interactions. In viral replication, non-structural protein 5 (Nsp5), also termed main protease (M pro ), plays a dominant role in processing coronavirus-encoded polyproteins and is thus recognized as an ideal target of anti-coronavirus agents. However, no structure of the MHV-A59 M pro has been reported, and molecular exploration of the catalysis mechanism remains hindered. Here, we solved the crystal structure of the MHV-A59 M pro complexed with a Michael acceptor-based inhibitor, N3. Structural analysis revealed that the Cβ of the vinyl group of N3 covalently bound to C145 of the catalytic dyad of M pro , which irreversibly inactivated cysteine protease activity. The lactam ring of the P1 side chain and the isobutyl group of the P2 side chain, which mimic the conserved residues at the same positions of the substrate, fit well into the S1 and S2 pockets. Through a comparative study with M pro of other coronaviruses, we observed that the substrate-recognition pocket and enzyme inhibitory mechanism is highly conservative. Altogether, our study provided structural features of MHV-A59 M pro and indicated that a Michael acceptor inhibitor is an ideal scaffold for antiviral drugs.

  • Organizational Affiliation

    School of Life Sciences, Tianjin University, Tianjin, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicative polyprotein 1abA [auth B],
B [auth C],
C [auth A]
301Murine hepatitis virus strain A59Mutation(s): 0 
Find proteins for P0C6X9 (Murine coronavirus (strain A59))
Explore P0C6X9 
Go to UniProtKB:  P0C6X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X9
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D, E, F
6synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.787α = 90
b = 64.034β = 125.97
c = 117.953γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFD0500300
Ministry of Science and Technology (China)China2015CB859800
National Natural Science Foundation of ChinaChina31528006

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Derived calculations
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations