2024Liu RNA

Citation

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography, Jianfang Liu, Ewan K.S. McRae, Meng Zhang, Cody Geary, Ebbe Sloth Andersen, Gang Ren, Nature Comm., (2024), 15, 9084. doi: 10.1038/s41467-024-52914-

Abstract

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e–Å−2, achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

Keywords

Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, RNA, self-folding

Paper links

https://www.nature.com/articles/s41467-024-52914-1

Related video

https://www.youtube.com/watch?v=AC_c1Mnh6ok https://www.youtube.com/watch?v=CuVR5ROj6Sg

Related methods

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249 https://www.nature.com/articles/s41598-018-34652-9 https://www.nature.com/articles/s41598-020-66793-1