6WQF

Structural Plasticity of the SARS-CoV-2 3CL Mpro Active Site Cavity Revealed by Room Temperature X-ray Crystallography

• PDB DOI: https://doi.org/10.2210/pdb6WQF/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-28 Released: 2020-05-06 
• Deposition Author(s): Kneller, D.W., Kovalevsky, A., Coates, L.
• Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.230 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Structural plasticity of SARS-CoV-2 3CL Mproactive site cavity revealed by room temperature X-ray crystallography.

Kneller, D.W., Phillips, G., O'Neill, H.M., Jedrzejczak, R., Stols, L., Langan, P., Joachimiak, A., Coates, L., Kovalevsky, A.

(2020) Nat Commun 11: 3202-3202

• PubMed: 32581217 
• DOI: https://doi.org/10.1038/s41467-020-16954-7
• Primary Citation of Related Structures:  
  6WQF


• PubMed Abstract: 
  

  The COVID-19 disease caused by the SARS-CoV-2 coronavirus has become a pandemic health crisis. An attractive target for antiviral inhibitors is the main protease 3CL M ^pro due to its essential role in processing the polyproteins translated from viral RNA. Here we report the room temperature X-ray structure of unliganded SARS-CoV-2 3CL M ^pro , revealing the ligand-free structure of the active site and the conformation of the catalytic site cavity at near-physiological temperature. Comparison with previously reported low-temperature ligand-free and inhibitor-bound structures suggest that the room temperature structure may provide more relevant information at physiological temperatures for aiding in molecular docking studies.

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Organizational Affiliation: 

Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.

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)

Macromolecule Content

• Total Structure Weight: 33.83 kDa 
• Atom Count: 2,420 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b 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: 2.30 Å
• R-Value Free: 0.230 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.065	α = 90
b = 54.063	β = 100.51
c = 113.601	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Kneller, D.W., Kovalevsky, A., Coates, L.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Database references, Structure summary
• Version 1.2: 2020-07-08
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description