Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

Kappel, Kalli; Zhang, Kaiming; Su, Zhaoming; Watkins, Andrew M.; Kladwang, Wipapat; Li, Shanshan; Pintilie, Grigore; Topkar, Ved V.; Rangan, Ramya; Zheludev, Ivan N.; Yesselman, Joseph D.; Chiu, Wah; Das, Rhiju

doi:10.1038/s41592-020-0878-9

Title: Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

Journal Article · Thu Jul 02 00:00:00 EDT 2020 · Nature Methods

DOI:https://doi.org/10.1038/s41592-020-0878-9· OSTI ID:1646882

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^[2]; Su, Zhaoming ^[3]; Watkins, Andrew M. ^[1]; Kladwang, Wipapat ^[1];

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^[2]; Topkar, Ved V. ^[1];

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^[1]; Yesselman, Joseph D. ^[4];

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Stanford Univ., CA (United States)
Stanford Univ., CA (United States). James H. Clark Center
Stanford Univ., CA (United States). James H. Clark Center; Sichuan Univ. (China). West China Hospital, State Key Lab. of Biotherapy
Stanford Univ., CA (United States); Univ. of Nebraska, Lincoln, NE (United States)
Stanford Univ., CA (United States); Stanford Univ., CA (United States). James H. Clark Center; SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. In this work, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. Furthermore ,this hybrid ‘Ribosolve’ pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC02-76SF00515; R01GM079429; R35 GM112579; P01AI120943; S10 OD021600; R21 AI145647; U54GM103297; P41GM103832; GRFP

OSTI ID:: 1646882

Journal Information:: Nature Methods, Vol. 17, Issue 7; ISSN 1548-7091

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 75 works

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References (55)

Structural insights into amino acid binding and gene control by a lysine riboswitch Serganov, Alexander; Huang, Lili; Patel, Dinshaw J. Nature, Vol. 455, Issue 7217 https://doi.org/10.1038/nature07326	journal	September 2008
Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena Kruger, Kelly; Grabowski, Paula J.; Zaug, Arthur J. Cell, Vol. 31, Issue 1 https://doi.org/10.1016/0092-8674(82)90414-7	journal	November 1982
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element Montange, Rebecca K.; Batey, Robert T. Nature, Vol. 441, Issue 7097 https://doi.org/10.1038/nature04819	journal	June 2006
Bacterial aptamers that selectively bind glutamine Ames, Tyler D.; Breaker, Ronald R. RNA Biology, Vol. 8, Issue 1 https://doi.org/10.4161/rna.8.1.13864	journal	January 2011
Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution Zhang, Kaiming; Li, Shanshan; Kappel, Kalli Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13494-7	journal	December 2019
SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ S Box/SAM-I Riboswitch Lu, Changrui; Ding, Fang; Chowdhury, Anirban Journal of Molecular Biology, Vol. 404, Issue 5 https://doi.org/10.1016/j.jmb.2010.09.059	journal	December 2010
Structural insights into recognition of c-di-AMP by the ydaO riboswitch Gao, Ang; Serganov, Alexander Nature Chemical Biology, Vol. 10, Issue 9 https://doi.org/10.1038/nchembio.1607	journal	August 2014
Structural basis for diversity in the SAM clan of riboswitches Trausch, J. J.; Xu, Z.; Edwards, A. L. Proceedings of the National Academy of Sciences, Vol. 111, Issue 18 https://doi.org/10.1073/pnas.1312918111	journal	April 2014
A complex ligase ribozyme evolved in vitro from a group I ribozyme domain Jaeger, L.; Wright, M. C.; Joyce, G. F. Proceedings of the National Academy of Sciences, Vol. 96, Issue 26 https://doi.org/10.1073/pnas.96.26.14712	journal	December 1999
De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes Kappel, Kalli; Liu, Shiheng; Larsen, Kevin P. Nature Methods, Vol. 15, Issue 11 https://doi.org/10.1038/s41592-018-0172-2	journal	October 2018
Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch Huang, L.; Ishibe-Murakami, S.; Patel, D. J. Proceedings of the National Academy of Sciences, Vol. 108, Issue 36 https://doi.org/10.1073/pnas.1111701108	journal	August 2011
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
Initial sequencing and analysis of the human genome Lander, Eric S.; Linton, Lauren M. Nature, Vol. 409, Issue 6822, p. 860-921 https://doi.org/10.1038/35057062	journal	February 2001
Animal snoRNAs and scaRNAs with exceptional structures Marz, Manja; Gruber, Andreas R.; Höner zu Siederdissen, Christian RNA Biology, Vol. 8, Issue 6 https://doi.org/10.4161/rna.8.6.16603	journal	November 2011
Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch Huang, Lili; Serganov, Alexander; Patel, Dinshaw J. Molecular Cell, Vol. 40, Issue 5 https://doi.org/10.1016/j.molcel.2010.11.026	journal	December 2010
Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies Russel, Daniel; Lasker, Keren; Webb, Ben PLoS Biology, Vol. 10, Issue 1 https://doi.org/10.1371/journal.pbio.1001244	journal	January 2012
Structure of the ternary initiation complex aIF2–GDPNP–methionylated initiator tRNA Schmitt, Emmanuelle; Panvert, Michel; Lazennec-Schurdevin, Christine Nature Structural & Molecular Biology, Vol. 19, Issue 4 https://doi.org/10.1038/nsmb.2259	journal	March 2012
Structure of the complete bacterial SRP Alu domain Kempf, Georg; Wild, Klemens; Sinning, Irmgard Nucleic Acids Research, Vol. 42, Issue 19 https://doi.org/10.1093/nar/gku883	journal	September 2014
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
Primerize: automated primer assembly for transcribing non-coding RNA domains Tian, Siqi; Yesselman, Joseph D.; Cordero, Pablo Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv538	journal	May 2015
Atomic accuracy in predicting and designing noncanonical RNA structure Das, Rhiju; Karanicolas, John; Baker, David Nature Methods, Vol. 7, Issue 4 https://doi.org/10.1038/nmeth.1433	journal	February 2010
Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing Cate, J. H.; Gooding, A. R.; Podell, E. Science, Vol. 273, Issue 5282 https://doi.org/10.1126/science.273.5282.1678	journal	September 1996
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR Kutchko, Katrina M.; Sanders, Wes; Ziehr, Ben RNA, Vol. 21, Issue 7 https://doi.org/10.1261/rna.049221.114	journal	May 2015
Large-scale determination of previously unsolved protein structures using evolutionary information Ovchinnikov, Sergey; Kinch, Lisa; Park, Hahnbeom eLife, Vol. 4 https://doi.org/10.7554/eLife.09248	journal	September 2015
Quantifying the local resolution of cryo-EM density maps Kucukelbir, Alp; Sigworth, Fred J.; Tagare, Hemant D. Nature Methods, Vol. 11, Issue 1 https://doi.org/10.1038/nmeth.2727	journal	November 2013
Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs Hangauer, Matthew J.; Vaughn, Ian W.; McManus, Michael T. PLoS Genetics, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pgen.1003569	journal	June 2013
Automated RNA Structure Prediction Uncovers a Kink-Turn Linker in Double Glycine Riboswitches Kladwang, Wipapat; Chou, Fang-Chieh; Das, Rhiju Journal of the American Chemical Society, Vol. 134, Issue 3 https://doi.org/10.1021/ja2093508	journal	January 2012
A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression Mandal, M. Science, Vol. 306, Issue 5694 https://doi.org/10.1126/science.1100829	journal	October 2004
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A. eLife, Vol. 5 https://doi.org/10.7554/eLife.17219	journal	September 2016
Crystal Structure of a Ten-Subunit Human Spliceosomal U1 snRNP at 5.5 Å Resolution Krummel, Daniel A. Pomeranz; Oubridge, Chris; Leung, Adelaine Biophysical Journal, Vol. 100, Issue 3 https://doi.org/10.1016/j.bpj.2010.12.1297	journal	February 2011
EMAN2: An extensible image processing suite for electron microscopy Tang, Guang; Peng, Liwei; Baldwin, Philip R. Journal of Structural Biology, Vol. 157, Issue 1 https://doi.org/10.1016/j.jsb.2006.05.009	journal	January 2007
Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy McMullan, G.; Faruqi, A. R.; Clare, D. Ultramicroscopy, Vol. 147 https://doi.org/10.1016/j.ultramic.2014.08.002	journal	December 2014
The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones Cech, Thomas R.; Steitz, Joan A. Cell, Vol. 157, Issue 1 https://doi.org/10.1016/j.cell.2014.03.008	journal	March 2014
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme Lehnert, Valerie; Jaeger, Luc; Michele, François Chemistry & Biology, Vol. 3, Issue 12 https://doi.org/10.1016/S1074-5521(96)90166-0	journal	December 1996
Amplification of RNA by an RNA polymerase ribozyme Horning, David P.; Joyce, Gerald F. Proceedings of the National Academy of Sciences, Vol. 113, Issue 35 https://doi.org/10.1073/pnas.1610103113	journal	August 2016
A Preorganized Active Site in the Crystal Structure of the Tetrahymena Ribozyme Golden, B. L. Science, Vol. 282, Issue 5387 https://doi.org/10.1126/science.282.5387.259	journal	October 1998
RELION: Implementation of a Bayesian approach to cryo-EM structure determination Scheres, Sjors H. W. Journal of Structural Biology, Vol. 180, Issue 3, p. 519-530 https://doi.org/10.1016/j.jsb.2012.09.006	journal	December 2012
Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies Ognjenović, Jana; Grisshammer, Reinhard; Subramaniam, Sriram Annual Review of Biomedical Engineering, Vol. 21, Issue 1 https://doi.org/10.1146/annurev-bioeng-060418-052453	journal	June 2019
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states Tian, Siqi; Cordero, Pablo; Kladwang, Wipapat RNA, Vol. 20, Issue 11 https://doi.org/10.1261/rna.044321.114	journal	September 2014
Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy Zhang, Huaqun; Keane, Sarah C. Wiley Interdisciplinary Reviews: RNA https://doi.org/10.1002/wrna.1541	journal	April 2019
Construction and Crystal Structure of Recombinant STNV Capsids Lane, Stephen W.; Dennis, Caitriona A.; Lane, Claire L. Journal of Molecular Biology, Vol. 413, Issue 1 https://doi.org/10.1016/j.jmb.2011.07.062	journal	October 2011
Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach Zhang, Kaiming; Keane, Sarah C.; Su, Zhaoming Structure, Vol. 26, Issue 3 https://doi.org/10.1016/j.str.2018.01.001	journal	March 2018
New molecular engineering approaches for crystallographic studies of large RNAs Zhang, Jinwei; Ferré-D’Amaré, Adrian R. Current Opinion in Structural Biology, Vol. 26 https://doi.org/10.1016/j.sbi.2014.02.001	journal	June 2014
An Assessment of the Precision and Accuracy of Protein Structures Determined by NMR Zhao, Daqing; Jardetzky, Oleg Journal of Molecular Biology, Vol. 239, Issue 5 https://doi.org/10.1006/jmbi.1994.1402	journal	June 1994
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches Weinberg, Z.; Regulski, E. E.; Hammond, M. C. RNA, Vol. 14, Issue 5 https://doi.org/10.1261/rna.988608	journal	March 2008
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions Li, Shuang; Su, Zhaoming; Lehmann, Jean Nature Structural & Molecular Biology, Vol. 26, Issue 12 https://doi.org/10.1038/s41594-019-0326-7	journal	November 2019
Computational design of three-dimensional RNA structure and function Yesselman, Joseph D.; Eiler, Daniel; Carlson, Erik D. Nature Nanotechnology, Vol. 14, Issue 9 https://doi.org/10.1038/s41565-019-0517-8	journal	August 2019
RNA design rules from a massive open laboratory Lee, Jeehyung; Kladwang, Wipapat; Lee, Minjae Proceedings of the National Academy of Sciences, Vol. 111, Issue 6 https://doi.org/10.1073/pnas.1313039111	journal	January 2014
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
RNA Mimics of Green Fluorescent Protein Paige, J. S.; Wu, K. Y.; Jaffrey, S. R. Science, Vol. 333, Issue 6042 https://doi.org/10.1126/science.1207339	journal	July 2011
Speciation of a group I intron into a lariat capping ribozyme Meyer, M.; Nielsen, H.; Olieric, V. Proceedings of the National Academy of Sciences, Vol. 111, Issue 21 https://doi.org/10.1073/pnas.1322248111	journal	May 2014
RNA structure inference through chemical mapping after accidental or intentional mutations Cheng, Clarence Y.; Kladwang, Wipapat; Yesselman, Joseph D. Proceedings of the National Academy of Sciences, Vol. 114, Issue 37 https://doi.org/10.1073/pnas.1619897114	journal	August 2017
Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch Butler, Ethan B.; Xiong, Yong; Wang, Jimin Chemistry & Biology, Vol. 18, Issue 3 https://doi.org/10.1016/j.chembiol.2011.01.013	journal	March 2011
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Serganov, Alexander; Huang, Lili; Patel, Dinshaw J. Nature, Vol. 458, Issue 7235 https://doi.org/10.1038/nature07642	journal	January 2009

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