Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemical Synthesis of Ligand NV-004
2.2. Chemical Synthesis of Fluorescent Protease Substrate
2.3. Protein Expression and Purification
2.4. Enzyme Kinetics and Inhibitor Activity Assays vs. Norovirus Protease
2.5. Crystallisation
2.6. Data Collection, Structural Determination and Refinement
2.7. Accession Number for Protein Structures
3. Results
3.1. Inhibitor Activity Analysis
3.2. Structure of the GII.4 Sydney 2012 HuNoV Protease in the Ligand-Free State
Conformation of Arg112
3.3. Structure of the GII.4 Sydney 2012 HuNoV Protease Bound to Inhibitor NV-004
Two Binding Sites for NV-004
- NV-004 site 1
- NV-004 site 2
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Data Collection | Ligand-Free | NV-004-Bound |
---|---|---|
Space group | C2221 | C2 |
Cell dimensions | ||
a, b, c (Å) | 112.8, 160.9, 95.3 | 79.4, 53.4, 50.0 |
α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 102.3, 90.0 |
Wavelength (Å) | 0.95364 | 0.95364 |
Resolution range (Å) | 2.79–48.54 (2.79–2.94) a | 1.84–48.85 (1.84–1.88) |
Observations | 143,659 (19,227) | 82,094 (4830) |
Unique reflections | 21,735 (2936) | 17,894 (1050) |
Rmerge (I) | 0.156 (1.26) | 0.037 (0.43) |
Rmeas (I) | 0.184 (1.48) | 0.047 (0.55) |
Rpim (I) | 0.097 (0.78) | 0.029 (0.34) |
Mean I/σ | 7.1 (1.0) | 14.2 (2.1) |
Mean CC1/2 | 0.994 (0.512) | 1.0 (0.85) |
Completeness (%) | 99.1 (93.9) | 99.7 (97.4) |
Multiplicity | 6.6 (6.5) | 4.6 (4.6) |
Protein chains in ASU | 4 | 1 |
No. of atoms | ||
Protein | 5006 | 1203 |
Ligands (all) | n/a | 79 |
NV004a | n/a | 33 |
NV004b | n/a | 23 |
Water | 9 | 102 |
Rwork | 0.194 | 0.165 |
Rfree | 0.214 | 0.191 |
RMSD from ideal | ||
Bond length (Å) | 0.002 | 0.006 |
Bond angle (°) | 0.483 | 0.900 |
Ramachandran Plot | ||
Favoured (%) | 96.8 | 98.7 |
Disfavoured (%) | 3.2 | 2.3 |
Outliers (%) | 0 | 0 |
Clash score (%-tile) b | 2.63 (100) | 1.62 (100) |
MolProbity score (%-tile) b | 1.25 (100) | 0.91 (100) |
B-factors (Å2) | ||
Average | 65.2 | 30.2 |
Protein | n/a | 29.5 |
Ligands (all) | n/a | 41.4 |
NV004a | n/a | 26.7 |
NV004b | n/a | 37.4 |
Water | 55.9 | 38.16 |
Occupancies (%) | ||
NV-004a | n/a | 100 |
NV-004b | n/a | 89 |
PDB ID | 8U1V | 8U1W |
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Eruera, A.-R.; McSweeney, A.M.; McKenzie-Goldsmith, G.M.; Opel-Reading, H.K.; Thomas, S.X.; Campbell, A.C.; Stubbing, L.; Siow, A.; Hubert, J.G.; Brimble, M.A.; et al. Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease. Viruses 2023, 15, 2202. https://doi.org/10.3390/v15112202
Eruera A-R, McSweeney AM, McKenzie-Goldsmith GM, Opel-Reading HK, Thomas SX, Campbell AC, Stubbing L, Siow A, Hubert JG, Brimble MA, et al. Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease. Viruses. 2023; 15(11):2202. https://doi.org/10.3390/v15112202
Chicago/Turabian StyleEruera, Alice-Roza, Alice M. McSweeney, Geena M. McKenzie-Goldsmith, Helen K. Opel-Reading, Simone X. Thomas, Ashley C. Campbell, Louise Stubbing, Andrew Siow, Jonathan G. Hubert, Margaret A. Brimble, and et al. 2023. "Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease" Viruses 15, no. 11: 2202. https://doi.org/10.3390/v15112202
APA StyleEruera, A.-R., McSweeney, A. M., McKenzie-Goldsmith, G. M., Opel-Reading, H. K., Thomas, S. X., Campbell, A. C., Stubbing, L., Siow, A., Hubert, J. G., Brimble, M. A., Ward, V. K., & Krause, K. L. (2023). Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease. Viruses, 15(11), 2202. https://doi.org/10.3390/v15112202