Adeno-Associated Virus (AAV-DJ)—Cryo-EM Structure at 1.56 Å Resolution
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Preparation
2.2. Image Acquisition
2.3. Image Processing
2.4. Atomic Modeling and Refinement
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Data Collection | |
---|---|
Magnification | 155,000× |
Voltage | 300 kV |
Electron exposure | 30 e−/Å2 |
Defocus range | −0.8 to −2.6 μm |
Pixel size | 0.514 Å |
(on refinement vs. atomic model:) | 0.5105 Å |
Data Processing | |
Motion correction | Relion 3.0 |
Anisotropic magnification correction | |
Distortion angle | 5.3° |
Percent distortion | 0.91% |
CTF estimation | |
Resolution range | 30 to 1.56 Å |
Symmetry imposed | I1 |
Initial particle images | 85,341 |
Final particle images | 48,209 |
Map resolution | 1.56 Å |
FSC threshold | 0.143 |
Protein atoms/asymmetric unit (mean B-factor): | 8144 (5.6 Å2) |
Non hydrogen | 4176 (5.3 Å2) |
Core β-barrel | 249 (3.3 Å2) |
Water molecules | 265 (11.9 Å2) |
RMS bond length deviation from ideal | 0.019 Å |
RMS bond angle deviation from ideal | 1.4° |
Ramachandran outliers | 1 (0.2%) |
Side chains: multiple conformer/outliers | 8/6 (1%) |
Cross-correlation (model-map) | 0.80 |
Resolution from model-map refinement (d0.5) | 1.44 Å (core β-barrel) |
Atoms | Cf. AAV-DJ at 4.5 Å (pdbID: 3J1Q) [20] | Cf. AAV-DJ at 2.8 Å resolution (pdbID: 5UF6) [22] |
All | 1.39 Å | 0.87 Å |
All, after rotamer inversion of (pseudo-) symmetrical side chains [58] | 1.36 Å | 0.80 Å |
After outliers removed (% atoms) | 1.06 (7%) | 0.35 Å (10%) |
ackbone | 0.96 Å | 0.42 Å |
After outliers removed (% atoms) | 0.87 (3%) | 0.29 Å (6%) |
Cα | 0.95 Å | 0.35 Å |
After outliers removed (% atoms) | 0.86 (3%) | 0.28 Å (5%) |
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Xie, Q.; Yoshioka, C.K.; Chapman, M.S. Adeno-Associated Virus (AAV-DJ)—Cryo-EM Structure at 1.56 Å Resolution. Viruses 2020, 12, 1194. https://doi.org/10.3390/v12101194
Xie Q, Yoshioka CK, Chapman MS. Adeno-Associated Virus (AAV-DJ)—Cryo-EM Structure at 1.56 Å Resolution. Viruses. 2020; 12(10):1194. https://doi.org/10.3390/v12101194
Chicago/Turabian StyleXie, Qing, Craig K. Yoshioka, and Michael S. Chapman. 2020. "Adeno-Associated Virus (AAV-DJ)—Cryo-EM Structure at 1.56 Å Resolution" Viruses 12, no. 10: 1194. https://doi.org/10.3390/v12101194