Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C2  (3D View)
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: 2434 
• Residue Count: 306 
• Unique protein chains: 1

7JUN

Joint neutron/X-ray structure of SARS-CoV-2 3CL Mpro at room temperature

• DOI: 10.2210/pdb7JUN/pdb

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


• Deposited: 2020-08-20 Released: 2020-09-02 
• Deposition Author(s): Kovalevsky, A., Kneller, D.W., Coates, L.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.220 
• R-Value Work: 0.185 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.253 
• R-Value Work: 0.201 

Literature

Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography.

Kneller, D.W., Phillips, G., Weiss, K.L., Pant, S., Zhang, Q., O'Neill, H.M., Coates, L., Kovalevsky, A.

(2020) J Biol Chem 295: 17365-17373

• PubMed: 33060199 
• DOI: 10.1074/jbc.AC120.016154
• Primary Citation of Related Structures:  
  7JUN


• PubMed Abstract: 
  

The main protease (3CL M ^pro ) from SARS-CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication. 3CL M ^pro possesses an unusual catalytic dyad composed of Cys ¹⁴⁵ and His ⁴¹ residues. A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active-site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus. Here, we present the room-temperature neutron structure of 3CL M ^pro , which allowed direct determination of hydrogen atom positions and, hence, protonation states in the protease. We observe that the catalytic site natively adopts a zwitterionic reactive form in which Cys ¹⁴⁵ is in the negatively charged thiolate state and His ⁴¹ is doubly protonated and positively charged, instead of the neutral unreactive state usually envisaged. The neutron structure also identified the protonation states, and thus electrical charges, of all other amino acid residues and revealed intricate hydrogen-bonding networks in the active-site cavity and at the dimer interface. The fine atomic details present in this structure were made possible by the unique scattering properties of the neutron, which is an ideal probe for locating hydrogen positions and experimentally determining protonation states at near-physiological temperature. Our observations provide critical information for structure-assisted and computational drug design, allowing precise tailoring of inhibitors to the enzyme's electrostatic environment.

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Organizational Affiliation: 

National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA.

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 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (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: 0.220 
• R-Value Work: 0.185 
• Space Group: C 1 2 1

• Method: NEUTRON DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.253 
• R-Value Work: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.927	α = 90
b = 54.686	β = 101.46
c = 45.216	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
PHASER	phasing
CrysalisPro	data reduction
CrysalisPro	data scaling
Mantid	data reduction
Mantid	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-08-20 
• Released Date: 2020-09-02 
Deposition Author(s): Kovalevsky, A., Kneller, D.W., Coates, L.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History 

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2020-12-23
  Changes: Database references