6JIJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.bbrc.2019.02.105
  • Primary Citation of Related Structures:  
    6JIJ

  • 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 mod ...

    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. Electronic address: zhanglei@tju.edu.cn.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
02J-ALA-VAL-LEU-PJE-010D, E, F6synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicative polyprotein 1abA, B, C301Murine hepatitis virus strain A59Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
Find proteins for P0C6X9 (Murine coronavirus (strain A59))
Explore P0C6X9 
Go to UniProtKB:  P0C6X9
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-21 
  • Released Date: 2019-04-24 
  • Deposition Author(s): Cui, W., Cui, S.S.

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 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Derived calculations