7YCH

Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicing

Summary for 7YCH

• Entry DOI: 10.2210/pdb7ych/pdb
• EMDB information: 33739
• Descriptor: RNA (5'-R(*CP*CP*CP*UP*CP*UP*AP*AP*AP*CP*C)-3'), RNA (393-MER), GUANOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: tetrahymena ribozyme, first step of self-splicing, conformation 3, rna
• Biological source: Tetrahymena; More
• Total number of polymer chains: 2
• Total formula weight: 130994.06

Authors

Zhang, X.,Li, S.,Pintilie, G.,Palo, M.Z.,Zhang, K. (deposition date: 2022-07-01, release date: 2023-07-05, Last modification date: 2023-08-16)

Primary citation

Zhang, X.,Li, S.,Pintilie, G.,Palo, M.Z.,Zhang, K.
Snapshots of the first-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM.
Nucleic Acids Res., 51:1317-1325, 2023

PubMed Abstract: 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.

PubMed: 36660826
DOI: 10.1093/nar/gkac1268

Experimental method

ELECTRON MICROSCOPY (3.09 Å)