Crystal Structure of the F140A mutant of SARS-Coronovirus 3C-like Protease at pH 6.5

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

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Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure.

Hu, T.Zhang, Y.Li, L.Wang, K.Chen, S.Chen, J.Ding, J.Jiang, H.Shen, X.

(2009) Virology 388: 324-334

  • DOI: https://doi.org/10.1016/j.virol.2009.03.034
  • Primary Citation of Related Structures:  
    3F9E, 3F9F, 3F9G, 3F9H

  • PubMed Abstract: 

    The 3C-like protease of SARS coronavirus (SARS-CoV 3CL(pro)) is vital for SARS-CoV replication and is a promising drug target. It has been extensively proved that only the dimeric enzyme is active. Here we discovered that two adjacent mutations (Ser139_Ala and Phe140_Ala) on the dimer interface resulted in completely different crystal structures of the enzyme, demonstrating the distinct roles of these two residues in maintaining the active conformation of SARS-CoV 3CL(pro). S139A is a monomer that is structurally similar to the two reported monomers G11A and R298A. However, this mutant still retains a small fraction of dimer in solution, which might account for its remaining activity. F140A is a dimer with the most collapsed active pocket discovered so far, well-reflecting the stabilizing role of this residue. Moreover, a plausible dimerization mechanism was also deduced from structural analysis. Our work is expected to provide insight on the dimerization-function relationship of SARS-CoV 3CL(pro).

  • Organizational Affiliation

    Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
303Severe acute respiratory syndrome-related coronavirusMutation(s): 1 
Gene Names: 1a
EC: 3.4.22
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Explore P0C6U8 
Go to UniProtKB:  P0C6U8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6U8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.248α = 90
b = 67.957β = 90
c = 149.286γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2023-12-27
    Changes: Data collection