EMD-45994

Single-particle
3.78 Å
EMD-45994 Deposition: 31/07/2024
Map released: 29/01/2025
Last modified: 05/02/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-45994

Small dataset reconstruction of the RaiA RNA motif

EMD-45994

Single-particle
3.78 Å
EMD-45994 Deposition: 31/07/2024
Map released: 29/01/2025
Last modified: 05/02/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Clostridium acetobutylicum
Sample: Bacterial RaiA RNA motif

Deposition Authors: Rudolfs B , Haack DB , Toor N
Scaffold-enabled high-resolution cryo-EM structure determination of RNA.
Haack DB , Rudolfs B , Jin S , Khitun A, Weeks KM , Toor N
(2025) Nat Commun , 16 , 880 - 880
PUBMED: 39837824
DOI: doi:10.1038/s41467-024-55699-5
ISSN: 2041-1723
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.