Movie
Controller
Structure viewers
About Yorodumi Papers
+Search query
-Structure paper
| Title | Scaffold-enabled high-resolution cryo-EM structure determination of RNA. |
|---|---|
| Journal, issue, pages | Nat Commun, Vol. 16, Issue 1, Page 880, Year 2025 |
| Publish date | Jan 21, 2025 |
 Authors | Daniel B Haack / Boris Rudolfs / Shouhong Jin / Alexandra Khitun / Kevin M Weeks / Navtej Toor /  |
| 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 ...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. |
 External links | Nat Commun / PubMed:39837824 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 2.41 - 4.73 Å |
| Structure data | EMDB-45247, PDB-9c6i: EMDB-45248, PDB-9c6j: EMDB-45249, PDB-9c6k:  EMDB-45250: Cryo-EM structure of the apo TPP riboswitch embedded in an RNA scaffold  EMDB-45251: Cryo-EM Structure of a group IIC intron embedded in an RNP scaffold  EMDB-45994: Small dataset reconstruction of the RaiA RNA motif |
| Chemicals |  ChemComp-MG:  ChemComp-TPP:  ChemComp-NA: |
| Source |
|
 Keywords | RNA / splicing / ribozyme / Intron / Riboswitch / Ligand |
oceanobacillus iheyensis (bacteria)
escherichia coli (E. coli)