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The SARS-CoV-2 frameshifting stimulatory element provides a representative case: cryo-EM captures a conformation with the slippery segment, whereas XRD reveals a higher-resolution, coaxially stacked structure lacking this segment but displaying base-triple interactions absent in cryo-EM. To reconcile these condition-dependent views, we integrate explicit-solvent molecular dynamics simulations with a structure-based electrostatic model (STEM) and show that Mg2+ ions drive transitions between these states by stabilizing long-range tertiary interactions involving the slippery site and stem3. Energy landscape analysis further reveals distinct folding pathways, while truncation of the slippery segment reshapes intermediates and yields pathways inconsistent with single-molecule optical tweezers experiments. The STEM framework demonstrates how information from condition-dependent experiments can be integrated to yield a coherent mechanistic picture of RNA folding.<\/jats:p>","DOI":"10.1021\/acs.jpclett.6c01457","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T21:22:13Z","timestamp":1788211333000},"page":"10199-10209","source":"Crossref","is-referenced-by-count":0,"title":["Reconciling\nCryo-EM and Crystallographic Views of\nRNA Folding through Atomistic Structure-Based Simulations: Roles of\nIonic Conditions and Truncation of Flexible Elements"],"prefix":"10.1021","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1264-3674","authenticated-orcid":true,"given":"Avijit","family":"Mainan","sequence":"first","affiliation":[{"name":"Indian Institute of Science Education and Research Kolkata , , , ,","place":["Mohanpur, West Bengal, India, 741246"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8380-5725","authenticated-orcid":true,"given":"Serdal","family":"Kirmizialtin","sequence":"additional","affiliation":[{"name":"New York University Abu Dhabi , , ,","place":["Abu Dhabi, United Arab Emirates, 129188"]},{"name":"New York University , , , ,","place":["New York, New York, United States, 10003"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6411-4347","authenticated-orcid":true,"given":"Susmita","family":"Roy","sequence":"additional","affiliation":[{"name":"Indian Institute of Science Education and Research Kolkata , , , ,","place":["Mohanpur, West Bengal, India, 741246"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"issue":"5","key":"2026090315420690500_cit1","doi-asserted-by":"publisher","first-page":"2345","DOI":"10.1042\/BST20210431","article-title":"Structure Determination of GPCRs: Cryo-EM Compared\nwith X-Ray Crystallography","volume":"49","author":"Garci\u0301a-Nafri\u0301a","year":"2021","journal-title":"Biochem. 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Y.; Roy, S.\n          Structural\nTopology-Based\nElectrostatic Model (STEM) Reveals Ion-Coordination Exchange as a\nDriver of RNA Folding Dynamics.  bioRxiv2026,10.64898\/2026.06.27.734987.","DOI":"10.64898\/2026.06.27.734987"},{"issue":"40","key":"2026090315420690500_cit45","doi-asserted-by":"publisher","first-page":"9680","DOI":"10.1021\/acs.jpcb.4c03981","article-title":"Magnesium Regulates\nRNA Ring Dynamics and Folding in Subgenomic Flaviviral RNA","volume":"128","author":"Mainan","year":"2024","journal-title":"J. Phys. Chem. 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Biol.\nChem."}],"container-title":["The Journal of Physical\nChemistry Letters"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jpclett.6c01457","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jpclcd\/article-pdf\/17\/35\/10199\/67392587\/acs.jpclett.6c01457.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jpclcd\/article-pdf\/17\/35\/10199\/67392587\/acs.jpclett.6c01457.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T19:42:14Z","timestamp":1788464534000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jpclcd\/article\/17\/35\/10199\/5328207\/Reconciling-Cryo-EM-and-Crystallographic-Views-of"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,24]]},"references-count":53,"journal-issue":{"issue":"35","published-online":{"date-parts":[[2026,8,24]]},"published-print":{"date-parts":[[2026,9,3]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jpclett.6c01457","relation":{},"ISSN":["1948-7185"],"issn-type":[{"value":"1948-7185","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,24]]}}}