Download MendeleyScaffold-enabled high-resolution cryo-EM structure determination of RNA.
Haack, D.B., Rudolfs, B., Jin, S., Khitun, A., Weeks, K.M., Toor, N.(2025) Nat Commun 16: 880-880
- PubMed: 39837824
- DOI: https://doi.org/10.1038/s41467-024-55699-5
- Primary Citation of Related Structures:
9C6I, 9C6J, 9C6K - PubMed Abstract:
Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail. These difficulties are compounded for small RNAs as cryo-EM is inherently more difficult for lower molecular weight macromolecules. Here we present a strategy for fusing small RNAs to a group II intron that yields high resolution structures of the appended RNA. We demonstrate this technology by determining the structures of the 86-nucleotide (nt) thiamine pyrophosphate (TPP) riboswitch aptamer domain and the recently described 210-nt raiA bacterial non-coding RNA involved in sporulation and biofilm formation. In the case of the TPP riboswitch aptamer domain, the scaffolding approach allowed visualization of the riboswitch ligand binding pocket at 2.5 Å resolution. We also determined the structure of the ligand-free apo state and observe that the aptamer domain of the riboswitch adopts an open Y-shaped conformation in the absence of ligand. Using this scaffold approach, we determined the structure of raiA at 2.5 Å in the core. Our versatile scaffolding strategy enables efficient RNA structure determination for a broad range of small to moderate-sized RNAs, which were previously intractable for high-resolution cryo-EM studies.
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
Organizational Affiliation:
