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TitleSnapshots of the first-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 3, Page 1317-1325, Year 2023
Publish dateFeb 22, 2023
AuthorsXiaojing Zhang / Shanshan Li / Grigore Pintilie / Michael Z Palo / Kaiming Zhang /
PubMed AbstractTetrahymena ribozyme is a group I intron, whose self-splicing is the result of two sequential ester-transfer reactions. To understand how it facilitates catalysis in the first self-splicing reaction, ...Tetrahymena ribozyme is a group I intron, whose self-splicing is the result of two sequential ester-transfer reactions. To understand how it facilitates catalysis in the first self-splicing reaction, we used cryogenic electron microscopy (cryo-EM) to resolve the structures of L-16 Tetrahymena ribozyme complexed with a 11-nucleotide 5'-splice site analog substrate. Four conformations were achieved to 4.14, 3.18, 3.09 and 2.98 Å resolutions, respectively, corresponding to different splicing intermediates during the first enzymatic reaction. Comparison of these structures reveals structural alterations, including large conformational changes in IGS/IGSext (P1-P1ext duplex) and J5/4, as well as subtle local rearrangements in the G-binding site. These structural changes are required for the enzymatic activity of the Tetrahymena ribozyme. Our study demonstrates the ability of cryo-EM to capture dynamic RNA structural changes, ushering in a new era in the analysis of RNA structure-function by cryo-EM.
External linksNucleic Acids Res / PubMed:36660826 / PubMed Central
MethodsEM (single particle)
Resolution2.98 - 4.14 Å
Structure data

33736

7yc8

EMDB-33736, PDB-7yc8:
Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicing
Method: EM (single particle) / Resolution: 4.14 Å

33738

7ycg

EMDB-33738, PDB-7ycg:
Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing
Method: EM (single particle) / Resolution: 3.18 Å

33739

7ych

EMDB-33739, PDB-7ych:
Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicing
Method: EM (single particle) / Resolution: 3.09 Å

33740

7yci

EMDB-33740, PDB-7yci:
Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the first-step self-splicing
Method: EM (single particle) / Resolution: 2.98 Å

Chemicals

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • tetrahymena (eukaryote)
KeywordsRNA / Tetrahymena ribozyme / first step of self-splicing / conformation 1 / conformation 2 / conformation 3 / conformation 4

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