9CXF

Cryo-EM structure of the Rail RNA motif

Summary for 9CXF

• Entry DOI: 10.2210/pdb9cxf/pdb
• EMDB information: 45988
• Descriptor: RNA (200-MER), MAGNESIUM ION (2 entities in total)
• Functional Keywords: non-coding rna, cryo-em, structural biology, rna
• Biological source: Clostridium acetobutylicum
• Total number of polymer chains: 1
• Total formula weight: 192557.65

Authors

Rudolfs, B.,Haack, D.B.,Toor, N. (deposition date: 2024-07-31, release date: 2025-01-29, Last modification date: 2025-05-14)

Primary citation

Haack, D.B.,Rudolfs, B.,Jin, S.,Weeks, K.M.,Toor, N.
Scaffold-enabled high-resolution cryo-EM structure determination of RNA.
Biorxiv, 2024

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, which we demonstrate with the 86-nucleotide thiamine pyrophosphate (TPP) riboswitch, and visualizing 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 undergoes a large-scale conformational change upon ligand binding, illustrating how small molecule binding to an RNA can induce large effects on gene expression. This study both sets a new standard for cryo-EM riboswitch visualization and offers a versatile strategy applicable to a broad range of small to moderate-sized RNAs, which were previously intractable for high-resolution cryo-EM studies.

PubMed: 38915706
DOI: 10.1101/2024.06.10.598011

Experimental method

ELECTRON MICROSCOPY (3.02 Å)