Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d

Abudayyeh, 2017, RNA targeting with CRISPR-Cas13, Nature, 550, 280, 10.1038/nature24049 Abudayyeh, 2016, C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector, Science, 353, aaf5573, 10.1126/science.aaf5573 Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 Anantharaman, 2013, Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing, Biol. Direct, 8, 15, 10.1186/1745-6150-8-15 Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 Brouns, 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 960, 10.1126/science.1159689 Chalmers, 2006, Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry, Anal. Chem., 78, 1005, 10.1021/ac051294f Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. D Biol. Crystallogr., 66, 12, 10.1107/S0907444909042073 Cox, 2017, RNA editing with CRISPR-Cas13, Science, 358, 1019, 10.1126/science.aaq0180 Dahlman, 2015, Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease, Nat. Biotechnol., 33, 1159, 10.1038/nbt.3390 East-Seletsky, 2016, Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, 538, 270, 10.1038/nature19802 Emsley, 2010, Features and development of Coot, Acta Crystallogr. D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 Englander, 2006, Hydrogen exchange and mass spectrometry: A historical perspective, J. Am. Soc. Mass Spectrom., 17, 1481, 10.1016/j.jasms.2006.06.006 Garcia-Doval, 2017, Molecular architectures and mechanisms of Class 2 CRISPR-associated nucleases, Curr. Opin. Struct. Biol., 47, 157, 10.1016/j.sbi.2017.10.015 Gootenberg, 2017, Nucleic acid detection with CRISPR-Cas13a/C2c2, Science, 356, 438, 10.1126/science.aam9321 Grant, 2015, Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6, eLife, 4, e06980, 10.7554/eLife.06980 Grant, 2018, cisTEM, user-friendly software for single-particle image processing, eLife, 7, e35383, 10.7554/eLife.35383 Hale, 2009, RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell, 139, 945, 10.1016/j.cell.2009.07.040 Han, 2014, Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response, Science, 343, 1244, 10.1126/science.1249845 Hohn, 2007, SPARX, a new environment for Cryo-EM image processing, J Struct Biol., 157, 47, 10.1016/j.jsb.2006.07.003 Hsu, 2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat. Biotechnol., 31, 827, 10.1038/nbt.2647 Jiang, 2016, Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity, Cell, 164, 710, 10.1016/j.cell.2015.12.053 Jinek, 2014, Structures of Cas9 endonucleases reveal RNA-mediated conformational activation, Science, 343, 1247997, 10.1126/science.1247997 Kazlauskiene, 2017, A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems, Science, 357, 605, 10.1126/science.aao0100 Keppel, 2015, Mapping residual structure in intrinsically disordered proteins at residue resolution using millisecond hydrogen/deuterium exchange and residue averaging, J. Am. Soc. Mass Spectrom., 26, 547, 10.1007/s13361-014-1033-6 Kiani, 2015, Cas9 gRNA engineering for genome editing, activation and repression, Nat. Methods, 12, 1051, 10.1038/nmeth.3580 Kimanius, 2016, Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2, eLife, 5, e18722, 10.7554/eLife.18722 Knott, 2017, Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme, Nat. Struct. Mol. Biol., 24, 825, 10.1038/nsmb.3466 Konermann, 2018, Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors, Cell, 173, 665, 10.1016/j.cell.2018.02.033 Koonin, 2017, Diversity, classification and evolution of CRISPR-Cas systems, Curr. Opin. Microbiol., 37, 67, 10.1016/j.mib.2017.05.008 Lander, 2009, Appion: an integrated, database-driven pipeline to facilitate EM image processing, J. Struct. Biol., 166, 95, 10.1016/j.jsb.2009.01.002 Liu, 2017, The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a, Cell, 170, 714, 10.1016/j.cell.2017.06.050 Liu, 2017, Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities, Cell, 168, 121, 10.1016/j.cell.2016.12.031 Lu, 2014, Three-dimensional structure of human γ-secretase, Nature, 512, 166, 10.1038/nature13567 Niewoehner, 2017, Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers, Nature, 548, 543, 10.1038/nature23467 Niewoehner, 2016, Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6, RNA, 22, 318, 10.1261/rna.054098.115 Nishimasu, 2015, Crystal Structure of Staphylococcus aureus Cas9, Cell, 162, 1113, 10.1016/j.cell.2015.08.007 Nishimasu, 2014, Crystal structure of Cas9 in complex with guide RNA and target DNA, Cell, 156, 935, 10.1016/j.cell.2014.02.001 Pascal, 2012, HDX workbench: software for the analysis of H/D exchange MS data, J. Am. Soc. Mass Spectrom., 23, 1512, 10.1007/s13361-012-0419-6 Pettersen, 2004, UCSF Chimera--a visualization system for exploratory research and analysis, J Comput Chem., 25, 1605, 10.1002/jcc.20084 Rohou, 2015, CTFFIND4: Fast and accurate defocus estimation from electron micrographs, J. Struct. Biol., 192, 216, 10.1016/j.jsb.2015.08.008 Roseman, 2004, FindEM--a fast, efficient program for automatic selection of particles from electron micrographs, J. Struct. Biol., 145, 91, 10.1016/j.jsb.2003.11.007 Samai, 2015, Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity, Cell, 161, 1164, 10.1016/j.cell.2015.04.027 Scheres, 2012, RELION: Implementation of a Bayesian approach to cryo-EM structure determination, J Struct Biol., 180, 519, 10.1016/j.jsb.2012.09.006 Shmakov, 2015, Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems, Mol. Cell, 60, 385, 10.1016/j.molcel.2015.10.008 Singh, 2018, Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a), Proc. Natl. Acad. Sci. USA, 115, 5444, 10.1073/pnas.1718686115 Smargon, 2017, Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28, Mol Cell, 65, 618, 10.1016/j.molcel.2016.12.023 Snijder, 2017, Vitrification after multiple rounds of sample application and blotting improves particle density on cryo-electron microscopy grids, J. Struct. Biol., 198, 38, 10.1016/j.jsb.2017.02.008 Sternberg, 2015, Conformational control of DNA target cleavage by CRISPR-Cas9, Nature, 527, 110, 10.1038/nature15544 Sternberg, 2014, DNA interrogation by the CRISPR RNA-guided endonuclease Cas9, Nature, 507, 62, 10.1038/nature13011 Suloway, 2005, Automated molecular microscopy: the new Leginon system, J. Struct. Biol., 151, 41, 10.1016/j.jsb.2005.03.010 Swarts, 2017, Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a, Mol Cell, 66, 221, 10.1016/j.molcel.2017.03.016 Tambe, 2018, RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a, Cell Rep., 24, 1025, 10.1016/j.celrep.2018.06.105 Tan, 2017, Addressing preferred specimen orientation in single-particle cryo-EM through tilting, Nat. Methods, 14, 793, 10.1038/nmeth.4347 Yan, 2018, Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein, Mol Cell, 70, 327, 10.1016/j.molcel.2018.02.028 Zhang, 2016, Gctf: Real-time CTF determination and correction, J. Struct. Biol., 193, 1, 10.1016/j.jsb.2015.11.003 Zhang, 1993, Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation, Protein Sci., 2, 522, 10.1002/pro.5560020404 Zheng, 2017, MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy, Nat. Methods, 14, 331, 10.1038/nmeth.4193