The SARS-CoV-2 Programmed ;#8722;1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09

Roman, Christina; Lewicka, Anna; Koirala, Deepak; Li, Nan-Sheng; Piccirilli, Joseph A.

doi:10.1021/acschembio.1c00324

The SARS-CoV-2 Programmed ;#8722;1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09

Journal Article · 01 July 2021 · ACS Chem. Biol.

DOI:https://doi.org/10.1021/acschembio.1c00324· OSTI ID:1821729

Roman, Christina; Lewicka, Anna; Koirala, Deepak; Li, Nan-Sheng; Piccirilli, Joseph A.

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH)

OSTI ID:: 1821729

Journal Information:: ACS Chem. Biol., Vol. 16, Issue (8)

Country of Publication:: United States

Language:: ENGLISH

References (46)

Principles for targeting RNA with drug-like small molecules Warner, Katherine Deigan; Hajdin, Christine E.; Weeks, Kevin M. Nature Reviews Drug Discovery, Vol. 17, Issue 8 https://doi.org/10.1038/nrd.2018.93	journal	July 2018
Targeting RNA structures in diseases with small molecules Shao, Yanqiu; Zhang, Qiangfeng Cliff Essays in Biochemistry, Vol. 64, Issue 6 https://doi.org/10.1042/EBC20200011	journal	December 2020
Anti-frameshifting Ligand Reduces the Conformational Plasticity of the SARS Virus Pseudoknot Ritchie, Dustin B.; Soong, Jingchyuan; Sikkema, William K. A. Journal of the American Chemical Society, Vol. 136, Issue 6 https://doi.org/10.1021/ja410344b	journal	January 2014
Programmed −1 Ribosomal Frameshifting in coronaviruses: A therapeutic target Kelly, Jamie A.; Woodside, Michael T.; Dinman, Jonathan D. Virology, Vol. 554 https://doi.org/10.1016/j.virol.2020.12.010	journal	February 2021
Anti-Frameshifting Ligand Active against SARS Coronavirus-2 Is Resistant to Natural Mutations of the Frameshift-Stimulatory Pseudoknot Neupane, Krishna; Munshi, Sneha; Zhao, Meng Journal of Molecular Biology, Vol. 432, Issue 21 https://doi.org/10.1016/j.jmb.2020.09.006	journal	October 2020
Identification of RNA Pseudoknot-Binding Ligand That Inhibits the −1 Ribosomal Frameshifting of SARS-Coronavirus by Structure-Based Virtual Screening Park, So-Jung; Kim, Yang-Gyun; Park, Hyun-Ju Journal of the American Chemical Society, Vol. 133, Issue 26 https://doi.org/10.1021/ja1098325	journal	July 2011
De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures Rangan, Ramya; Watkins, Andrew M.; Chacon, Jose Nucleic Acids Research, Vol. 49, Issue 6 https://doi.org/10.1093/nar/gkab119	journal	March 2021
Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers Omar, Sara Ibrahim; Zhao, Meng; Sekar, Rohith Vedhthaanth PLOS Computational Biology, Vol. 17, Issue 1 https://doi.org/10.1371/journal.pcbi.1008603	journal	January 2021
A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal Plant, Ewan P.; Pérez-Alvarado, Gabriela C.; Jacobs, Jonathan L. PLoS Biology, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pbio.0030172	journal	May 2005
Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins Plant, Ewan P.; Rakauskaitė, Rasa; Taylor, Deborah R. Journal of Virology, Vol. 84, Issue 9 https://doi.org/10.1128/JVI.02480-09	journal	February 2010
Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production Plant, Ewan; Sims, Amy; Baric, Ralph Viruses, Vol. 5, Issue 1 https://doi.org/10.3390/v5010279	journal	January 2013
Programmed ribosomal frameshifting in HIV-1 and the SARS–CoV Brierley, Ian; Dos Ramos, Francisco J. Virus Research, Vol. 119, Issue 1 https://doi.org/10.1016/j.virusres.2005.10.008	journal	July 2006
Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods Chang, Kai-Chun Computational and Mathematical Methods in Medicine, Vol. 2012 https://doi.org/10.1155/2012/569870	journal	January 2012
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use Atkins, John F.; Loughran, Gary; Bhatt, Pramod R. Nucleic Acids Research https://doi.org/10.1093/nar/gkw530	journal	July 2016
Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U 6 A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting Lin, Zhaoru; Gilbert, Robert J. C.; Brierley, Ian Nucleic Acids Research, Vol. 40, Issue 17 https://doi.org/10.1093/nar/gks629	journal	June 2012
RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus Ishimaru, Daniella; Plant, Ewan P.; Sims, Amy C. Nucleic Acids Research, Vol. 41, Issue 4 https://doi.org/10.1093/nar/gks1361	journal	December 2012
Translocation kinetics and structural dynamics of ribosomes are modulated by the conformational plasticity of downstream pseudoknots Wu, Bo; Zhang, Haibo; Sun, Ruirui Nucleic Acids Research, Vol. 46, Issue 18 https://doi.org/10.1093/nar/gky636	journal	July 2018
Programmed –1 Frameshifting by Kinetic Partitioning during Impeded Translocation Caliskan, Neva; Katunin, Vladimir I.; Belardinelli, Riccardo Cell, Vol. 157, Issue 7 https://doi.org/10.1016/j.cell.2014.04.041	journal	June 2014
Changed in translation: mRNA recoding by −1 programmed ribosomal frameshifting Caliskan, Neva; Peske, Frank; Rodnina, Marina V. Trends in Biochemical Sciences, Vol. 40, Issue 5 https://doi.org/10.1016/j.tibs.2015.03.006	journal	May 2015
Mechanisms and implications of programmed translational frameshifting: Mechanisms and implications of programmed translational frameshifting Dinman, Jonathan D. Wiley Interdisciplinary Reviews: RNA, Vol. 3, Issue 5 https://doi.org/10.1002/wrna.1126	journal	June 2012
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Complex dynamics under tension in a high-efficiency frameshift stimulatory structure Halma, Matthew T. J.; Ritchie, Dustin B.; Cappellano, Tonia R. Proceedings of the National Academy of Sciences, Vol. 116, Issue 39 https://doi.org/10.1073/pnas.1905258116	journal	August 2019
Programmed -1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding Ritchie, D. B.; Foster, D. A. N.; Woodside, M. T. Proceedings of the National Academy of Sciences, Vol. 109, Issue 40 https://doi.org/10.1073/pnas.1204114109	journal	September 2012
Conformational Shannon Entropy of mRNA Structures from Force Spectroscopy Measurements Predicts the Efficiency of − 1 Programmed Ribosomal Frameshift Stimulation Halma, Matthew T. J.; Ritchie, Dustin B.; Woodside, Michael T. Physical Review Letters, Vol. 126, Issue 3 https://doi.org/10.1103/PhysRevLett.126.038102	journal	January 2021
Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China Wu, Aiping; Peng, Yousong; Huang, Baoying Cell Host & Microbe, Vol. 27, Issue 3 https://doi.org/10.1016/j.chom.2020.02.001	journal	March 2020
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy Wacker, Anna; Weigand, Julia E.; Akabayov, Sabine R. Nucleic Acids Research, Vol. 48, Issue 22 https://doi.org/10.1093/nar/gkaa1013	journal	November 2020
Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2) Kelly, Jamie A.; Olson, Alexandra N.; Neupane, Krishna Journal of Biological Chemistry, Vol. 295, Issue 31 https://doi.org/10.1074/jbc.AC120.013449	journal	July 2020
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements Manfredonia, Ilaria; Nithin, Chandran; Ponce-Salvatierra, Almudena Nucleic Acids Research, Vol. 48, Issue 22 https://doi.org/10.1093/nar/gkaa1053	journal	November 2020
Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element Schlick, Tamar; Zhu, Qiyao; Jain, Swati Biophysical Journal, Vol. 120, Issue 6 https://doi.org/10.1016/j.bpj.2020.10.012	journal	March 2021
A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination Koldobskaya, Yelena; Duguid, Erica M.; Shechner, David M. Nature Structural & Molecular Biology, Vol. 18, Issue 1 https://doi.org/10.1038/nsmb.1945	journal	December 2010
Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation Koirala, Deepak; Lewicka, Anna; Koldobskaya, Yelena ACS Chemical Biology, Vol. 15, Issue 1 https://doi.org/10.1021/acschembio.9b00785	journal	November 2019
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3330	journal	November 2017
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
3′ end additions by T7 RNA polymerase are RNA self-templated, distributive and diverse in character—RNA-Seq analyses Gholamalipour, Yasaman; Karunanayake Mudiyanselage, Aruni; Martin, Craig T. Nucleic Acids Research, Vol. 46, Issue 18 https://doi.org/10.1093/nar/gky796	journal	September 2018
Ionic strength-dependent persistence lengths of single-stranded RNA and DNA Chen, H.; Meisburger, S. P.; Pabit, S. A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 3 https://doi.org/10.1073/pnas.1119057109	journal	December 2011
Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms Huston, Nicholas C.; Wan, Han; Strine, Madison S. Molecular Cell, Vol. 81, Issue 3 https://doi.org/10.1016/j.molcel.2020.12.041	journal	February 2021
Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting Chen, G.; Chang, K. -Y.; Chou, M. -Y. Proceedings of the National Academy of Sciences, Vol. 106, Issue 31 https://doi.org/10.1073/pnas.0905046106	journal	July 2009
Frameshifting RNA pseudoknots: Structure and mechanism Giedroc, David P.; Cornish, Peter V. Virus Research, Vol. 139, Issue 2 https://doi.org/10.1016/j.virusres.2008.06.008	journal	February 2009
Structural Dynamics of SARS-CoV-2 Frameshift Signal Studied by Single-Molecule Force Spectroscopy Reveal Topologically Distinct Conformers Neupane, Krishna P.; Zhao, Meng; Hoffer, Noel Q. Biophysical Journal, Vol. 120, Issue 3 https://doi.org/10.1016/j.bpj.2020.11.1987	journal	February 2021
Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0107504	journal	September 2014
Expression and Purification of Active Recombinant T7 RNA Polymerase from E. coli Rio, D. C. Cold Spring Harbor Protocols, Vol. 2013, Issue 11 https://doi.org/10.1101/pdb.prot078527	journal	November 2013
3′-End Labeling of RNA with [5′- ³² P]Cytidine 3′,5′-Bis(Phosphate) and T4 RNA Ligase 1 Nilsen, Timothy W. Cold Spring Harbor Protocols, Vol. 2014, Issue 4 https://doi.org/10.1101/pdb.prot080713	journal	April 2014
The architecture of the SARS-CoV-2 RNA genome inside virion Cao, Changchang; Cai, Zhaokui; Xiao, Xia Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22785-x	journal	June 2021
The E Protein Is a Multifunctional Membrane Protein of SARS-CoV Wu, Qingfa; Zhang, Yilin; Lü, Hong Genomics, Proteomics & Bioinformatics, Vol. 1, Issue 2 https://doi.org/10.1016/S1672-0229(03)01017-9	journal	May 2003

Similar Records

Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)

Journal Article · 2021 · Journal of Biological Chemistry · OSTI ID:1690151

Kelly, J; Olson, A.; Neupane, K.; +5 more

Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)

Journal Article · 2020 · Journal of Biological Chemistry · OSTI ID:1769486

Kelly, Jamie A.; Olson, Alexandra N.; Neupane, Krishna; +5 more

Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting

Journal Article · 2022 · RNA · OSTI ID:1844713

Jones, Christopher P.; Ferre-D'Amare, Adrian R.

The SARS-CoV-2 Programmed ;#8722;1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09

Citation Formats

References (46)

Similar Records

Related Subjects