Crystal structure of native SARS CLpro

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

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Understanding the maturation process and inhibitor design of SARS-CoV 3CLpro from the crystal structure of C145A in a product-bound form

Hsu, M.F.Kuo, C.J.Fang, J.M.Shie, J.J.Chang, K.T.Chang, H.C.Chou, C.C.Ko, T.P.Shr, H.L.Chang, G.G.Wu, Y.T.Wang, A.H.Liang, P.H.

(2005) J Biol Chem 280: 31257-31266

  • DOI: https://doi.org/10.1074/jbc.M502577200
  • Primary Citation of Related Structures:  
    1Z1I, 1Z1J

  • PubMed Abstract: 

    Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by a novel human coronavirus. Viral maturation requires a main protease (3CL(pro)) to cleave the virus-encoded polyproteins. We report here that the 3CL(pro) containing additional N- and/or C-terminal segments of the polyprotein sequences undergoes autoprocessing and yields the mature protease in vitro. The dimeric three-dimensional structure of the C145A mutant protease shows that the active site of one protomer binds with the C-terminal six amino acids of the protomer from another asymmetric unit, mimicking the product-bound form and suggesting a possible mechanism for maturation. The P1 pocket of the active site binds the Gln side chain specifically, and the P2 and P4 sites are clustered together to accommodate large hydrophobic side chains. The tagged C145A mutant protein served as a substrate for the wild-type protease, and the N terminus was first digested (55-fold faster) at the Gln(-1)-Ser1 site followed by the C-terminal cleavage at the Gln306-Gly307 site. Analytical ultracentrifuge of the quaternary structures of the tagged and mature proteases reveals the remarkably tighter dimer formation for the mature enzyme (K(d) = 0.35 nm) than for the mutant (C145A) containing 10 extra N-terminal (K(d) = 17.2 nM) or C-terminal amino acids (K(d) = 5.6 nM). The data indicate that immature 3CL(pro) can form dimer enabling it to undergo autoprocessing to yield the mature enzyme, which further serves as a seed for facilitated maturation. Taken together, this study provides insights into the maturation process of the SARS 3CL(pro) from the polyprotein and design of new structure-based inhibitors.

  • Organizational Affiliation

    Institute of Biochemical Sciences, National Taiwan University, Taipei 106.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
EC: 3.4.22
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
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UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.19α = 90
b = 45.06β = 90
c = 53.99γ = 90

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references