8E4J | pdb_00008e4j

Room-temperature X-ray structure of SARS-CoV-2 main protease H41A miniprecursor mutant

• PDB DOI: https://doi.org/10.2210/pdb8E4J/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-08-18 Released: 2022-11-23 
• Deposition Author(s): Coates, L., Kneller, D.W., Kovalevsky, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor.

Kovalevsky, A., Coates, L., Kneller, D.W., Ghirlando, R., Aniana, A., Nashed, N.T., Louis, J.M.

(2022) J Mol Biology 434: 167876-167876

• PubMed: 36334779 
• DOI: https://doi.org/10.1016/j.jmb.2022.167876
• Primary Citation Related Structures: 
  8E4J, 8E4R


• PubMed Abstract: 
  

  We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (T _m ) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [ ^(-6) MPro ^H41A and ^(-6*) MPro ^H41A , respectively], and its corresponding mature MPro ^H41A were systematically examined. While the H41A mutation exerts negligible effect on T _m and dimer dissociation constant (K _dimer ) of MPro ^H41A , relative to the wild type MPro, both miniprecursors show a 4-5 °C decrease in T _m and > 85-fold increase in K _dimer as compared to MPro ^H41A . The K _d for the binding of the covalent inhibitor GC373 to ^(-6*) MPro ^H41A increases ∼12-fold, relative to MPro ^H41A , concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers' oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Disorder of the terminal residues 1-2 and 302-306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.

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Organizational Affiliation: 
• Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA. Electronic address: [e-mail].
Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA. Electronic address: https://www.twitter.com/DanielKneller.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA.
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA.
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA. Electronic address: [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)

Macromolecule Content 

• Total Structure Weight: 69.01 kDa 
• Atom Count: 4,883 
• Modeled Residue Count: 598 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A, B	314	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2  Gene Names: rep, 1a-1b
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: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.094	α = 90
b = 99.817	β = 108.1
c = 59.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Coates, L., Kneller, D.W., Kovalevsky, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2022-11-30
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description