7BRO | pdb_00007bro

Crystal structure of the 2019-nCoV main protease

• PDB DOI: https://doi.org/10.2210/pdb7BRO/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-03-29 Released: 2020-05-13 
• Deposition Author(s): Fu, L.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease.

Fu, L., Ye, F., Feng, Y., Yu, F., Wang, Q., Wu, Y., Zhao, C., Sun, H., Huang, B., Niu, P., Song, H., Shi, Y., Li, X., Tan, W., Qi, J., Gao, G.F.

(2020) Nat Commun 11: 4417-4417

• PubMed: 32887884 
• DOI: https://doi.org/10.1038/s41467-020-18233-x
• Primary Citation Related Structures: 
  7BRO, 7BRP, 7C6S, 7C6U, 7D1M


• PubMed Abstract: 
  

  COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (M ^pro , also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clinically approved anti-HCV drug, Boceprevir, and a pre-clinical inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting M ^pro . Moreover, combined application of GC376 with Remdesivir, a nucleotide analogue that inhibits viral RNA dependent RNA polymerase (RdRp), results in sterilizing additive effect. Further structural analysis reveals binding of both inhibitors to the catalytically active side of SARS-CoV-2 protease M ^pro as main mechanism of inhibition. Our findings may provide critical information for the optimization and design of more potent inhibitors against the emerging SARS-CoV-2 virus.

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Organizational Affiliation: 
• CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, 100101, Beijing, China.
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China.
University of Chinese Academy of Sciences, 100049, Beijing, China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201204, Shanghai, China.
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China.
Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, China.
Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, 100049, Beijing, China. [e-mail].
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control & Prevention, Chinese Center for Disease Control and Prevention, China CDC, 102206, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].
Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.88 kDa 
• Atom Count: 2,463 
• Modeled Residue Count: 300 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	307	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.434	α = 90
b = 54.259	β = 100.671
c = 44.959	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Fu, L.F.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Database references
• Version 1.2: 2021-03-10
  Changes: Structure summary
• Version 1.3: 2023-11-29
  Changes: Data collection, Database references, Refinement description