Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro
Abstract
:1. Introduction
2. Results and Discussion
2.1. Structural Properties of the Catalytic Domain of SARS-CoV-2 3CLpro
2.2. Enzymatic Properties of the Monomeric Form of the Catalytic Domain
2.3. Structural Comparison among Various 3CLpros
3. Materials and Methods
3.1. Protein Expression and Purification of SARS-CoV-2 3CLpro and its Catalytic Domain
3.2. Enzymatic Kinetic Studies with SARS-CoV-2 3CLpro
3.3. Size-Exlusion Chromatography (SEC)
3.4. Crystallization
3.5. Structure Determination
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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PDB Code | 7WHC |
---|---|
Data collection statistics | |
Wavelength | 1.0000 Å |
Resolution | 50.0–2.27 (2.31–2.27) Å |
Redundancy | 3.4 (3.1) * |
Unique reflections | 32201 (1203) |
Completeness | 89.0 (63.2) % |
I/σ | 17.03 (1.67) |
Rmergy † | 5.7 (63.2) % |
Crystal parameters and refinement statistics | |
Resolution | 31.99–2.27 (2.31–2.27) Å |
Space group | P21 |
Cell dimensions | 52.47 Å × 121.09 Å × 62.70 Å |
Volume fraction of solvent | 48.13% |
Vm (Å3/Dalton) | 2.37 |
Total number of residues | 5628 |
Total non-H atoms | 5778 |
Number of water molecules | 150 |
Average temperature factors | |
Protein | 48.90 Å2 |
Solvent | 45.70 Å2 |
R-factor | 20.16% |
Free R-factor | 26.41% |
Stereochemical ideality: | |
Bond | 0.009 Å |
Angle | 1.297° |
Chirality | 0.049° |
Planarity | 0.006° |
Dihedral | 13.954° |
Ramachandran plot | |
Residues in favored regions | 92.78% |
Residues in allowed regions | 6.94% |
Residues in disallowed regions | 0.0% |
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Jo, S.; Kim, H.Y.; Shin, D.H.; Kim, M.-S. Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro. Int. J. Mol. Sci. 2022, 23, 5268. https://doi.org/10.3390/ijms23095268
Jo S, Kim HY, Shin DH, Kim M-S. Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro. International Journal of Molecular Sciences. 2022; 23(9):5268. https://doi.org/10.3390/ijms23095268
Chicago/Turabian StyleJo, Seri, Hwa Young Kim, Dong Hae Shin, and Mi-Sun Kim. 2022. "Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro" International Journal of Molecular Sciences 23, no. 9: 5268. https://doi.org/10.3390/ijms23095268
APA StyleJo, S., Kim, H. Y., Shin, D. H., & Kim, M. -S. (2022). Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro. International Journal of Molecular Sciences, 23(9), 5268. https://doi.org/10.3390/ijms23095268