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TitleScaffold-enabled high-resolution cryo-EM structure determination of RNA.
Journal, issue, pagesbioRxiv, Year 2024
Publish dateJun 10, 2024
AuthorsDaniel B Haack / Boris Rudolfs / Shouhong Jin / Kevin M Weeks / Navtej Toor /
PubMed AbstractCryo-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, 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.
External linksbioRxiv / PubMed:38915706 / PubMed Central
MethodsEM (single particle)
Resolution3.02 Å
Structure data

45988

9cxf

EMDB-45988, PDB-9cxf:
Cryo-EM structure of the Rail RNA motif
Method: EM (single particle) / Resolution: 3.02 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • clostridium acetobutylicum (bacteria)
KeywordsRNA / non-coding RNA / cryo-EM / structural biology

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