Structural Insights into the Dynamic Assembly of a YFV sNS1 Tetramer
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. Construction, Expression, and Purification of YFV NS1
2.3. CryoEM Grid Preparation and Data Collection
2.4. CryoEM Data Processing of YFV NS1
2.5. Model Building and Refinement
3. Results
3.1. CryoEM Structures Analysis of YFV sNS1 Oligomers
3.2. The Assembly of YFV sNS1 Tetramer
3.3. The YFV Tetramer Is a Semi-Stable Structure
3.4. The Dynamic Characteristics of YFV NS1 Tetramer
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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YFV_NS1 Focused Dimer (EMDB: 39898) (PDB: 8ZB9) | YFV_NS1_tetramer (EMDB: 39899) (PDB: 8ZBA) | |
---|---|---|
Data and processing | v | |
Magnification | 105,000 | 105,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e−/Å2) | 50 | 50 |
Defocus range (μm) | −1.2~−1.8 | −1.2~−1.8 |
Pixel size (Å) | 0.85 | 0.85 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 4,793,330 | 4,793,330 |
Final particle images (no.) | 215,543 | 215,543 |
Map resolution (Å) | 3.31 | 3.57 |
FSC threshold | 0.143 | 0.143 |
Map resolution range | 3.0–4.5 | 3.0–5.0 |
Refinement | ||
Initial model used (PDB code) | - | - |
Map sharpening B factor (Å2) | −172.8 | −183.0 |
Model composition | ||
Non-hydrogen atoms | 4912 | 9804 |
Protein residues | 623 | 1244 |
Ligands | - | - |
B factor (Å2) | ||
Protein | 54.32 | 54.32 |
Ligand | - | - |
R.m.s. deviations | ||
Bond lengths (Å) | 0.006 | 0.007 |
Bond angles (°) | 0.830 | 0.893 |
Validation | ||
MolProbity score | 2.33 | 2.40 |
Clash score | 14.87 | 7.10 |
Rotamers outliers (%) | 0.00 | 0.92 |
Ramachandra plot | ||
Favored | 85.50 | 89.28 |
Allowed | 14.33 | 14.98 |
Outliers | 0.16 | 0.00 |
Model-map FSC (0.143) | 3.43 | 3.78 |
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Pan, Q.; Chen, Q.; Zhang, W.; Jiao, H.; Yu, L.; Hu, H. Structural Insights into the Dynamic Assembly of a YFV sNS1 Tetramer. Viruses 2024, 16, 1212. https://doi.org/10.3390/v16081212
Pan Q, Chen Q, Zhang W, Jiao H, Yu L, Hu H. Structural Insights into the Dynamic Assembly of a YFV sNS1 Tetramer. Viruses. 2024; 16(8):1212. https://doi.org/10.3390/v16081212
Chicago/Turabian StylePan, Qi, Qiang Chen, Wanqin Zhang, Haizhan Jiao, Lei Yu, and Hongli Hu. 2024. "Structural Insights into the Dynamic Assembly of a YFV sNS1 Tetramer" Viruses 16, no. 8: 1212. https://doi.org/10.3390/v16081212
APA StylePan, Q., Chen, Q., Zhang, W., Jiao, H., Yu, L., & Hu, H. (2024). Structural Insights into the Dynamic Assembly of a YFV sNS1 Tetramer. Viruses, 16(8), 1212. https://doi.org/10.3390/v16081212