Tal, N. & Sorek, R. SnapShot: bacterial immunity. Cell 185, 578–578 e571 (2022).
Article CAS PubMed Google Scholar
Koonin, E. V., Makarova, K. S. & Zhang, F. Diversity, classification and evolution of CRISPR–Cas systems. Curr. Opin. Microbiol. 37, 67–78 (2017).
Article CAS PubMed PubMed Central Google Scholar
Duncan-Lowey, B. & Kranzusch, P. J. CBASS phage defense and evolution of antiviral nucleotide signaling. Curr. Opin. Immunol. 74, 156–163 (2022).
Article CAS PubMed Google Scholar
Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science https://doi.org/10.1126/science.aar4120 (2018).
Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084 (2020).
Article CAS PubMed PubMed Central Google Scholar
Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556–1569 e1555 (2022).
Article CAS PubMed Google Scholar
Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).
Article CAS PubMed PubMed Central Google Scholar
Cheng, R. et al. A nucleotide-sensing endonuclease from the Gabija bacterial defense system. Nucleic Acids Res. 49, 5216–5229 (2021).
Article CAS PubMed PubMed Central Google Scholar
Cheng, R. et al. Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense. Cell Host Microbe https://doi.org/10.1016/j.chom.2023.06.014 (2023).
Article PubMed PubMed Central Google Scholar
Liu, Y. et al. ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex. EMBO J. 35, 743–758 (2016).
Article CAS PubMed Google Scholar
Hopfner, K. P. et al. Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily. Cell 101, 789–800 (2000).
Article CAS PubMed Google Scholar
Aravind, L., Leipe, D. D. & Koonin, E. V. Toprim—a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res. 26, 4205–4213 (1998).
Article CAS PubMed PubMed Central Google Scholar
Schiltz, C. J., Lee, A., Partlow, E. A., Hosford, C. J. & Chappie, J. S. Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Nucleic Acids Res. 47, 9448–9463 (2019).
Article CAS PubMed PubMed Central Google Scholar
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Article CAS PubMed PubMed Central Google Scholar
Antine, S. P. et al. Structural basis of Gabija anti-phage defence and viral immune evasion. Nature https://doi.org/10.1038/s41586-023-06855-2 (2023).
Article PubMed PubMed Central Google Scholar
Schiltz, C. J., Adams, M. C. & Chappie, J. S. The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. Nucleic Acids Res. 48, 2762–2776 (2020).
Article CAS PubMed PubMed Central Google Scholar
Baek, M. et al. Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA. Nat. Methods https://doi.org/10.1038/s41592-023-02086-5 (2023).
Article PubMed PubMed Central Google Scholar
Korolev, S., Hsieh, J., Gauss, G. H., Lohman, T. M. & Waksman, G. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90, 635–647 (1997).
Article CAS PubMed Google Scholar
Velankar, S. S., Soultanas, P., Dillingham, M. S., Subramanya, H. S. & Wigley, D. B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75–84 (1999).
Article CAS PubMed Google Scholar
Lee, J. Y. & Yang, W. UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell 127, 1349–1360 (2006).
Article CAS PubMed PubMed Central Google Scholar
Duncan-Lowey, B. et al. Cryo-EM structure of the RADAR supramolecular anti-phage defense complex. Cell 186, 987–998 e915 (2023).
Article CAS PubMed PubMed Central Google Scholar
Gao, Y. et al. Molecular basis of RADAR anti-phage supramolecular assemblies. Cell 186, 999–1012 e1020 (2023).
Article CAS PubMed Google Scholar
Gao, L. A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).
Article CAS PubMed PubMed Central Google Scholar
Shen, Z., Lin, Q., Yang, X. Y., Fosuah, E. & Fu, T. M. Assembly-mediated activation of the SIR2-HerA supramolecular complex for anti-phage defense. Mol. Cell https://doi.org/10.1016/j.molcel.2023.11.007 (2023).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Article CAS PubMed Google Scholar
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
Article CAS PubMed Google Scholar
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Article CAS PubMed Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Article CAS PubMed PubMed Central Google Scholar
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
Article CAS PubMed Google Scholar
The PyMOL Molecular Graphics System, Version 3.0 (Schrödinger, 2022)
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Article CAS PubMed Google Scholar
Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. Enumeration of bacteriophages using the small drop plaque assay system. Methods Mol. Biol. 501, 81–85 (2009).
Article CAS PubMed Google Scholar
Kropinski, A. M., Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. Enumeration of bacteriophages by double agar overlay plaque assay. Methods Mol. Biol. 501, 69–76 (2009).
Article CAS PubMed Google Scholar
Marty, M. T. et al. Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. Anal. Chem. 87, 4370–4376 (2015).
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