7YGC

Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing

Summary for 7YGC

• Entry DOI: 10.2210/pdb7ygc/pdb
• EMDB information: 33815
• Descriptor: RNA (5'-R(*UP*CP*G)-3'), RNA (5'-R(*CP*CP*CP*UP*CP*UP*UP*AP*AP*CP*C)-3'), RNA (393-MER), ... (4 entities in total)
• Functional Keywords: tetrahymena ribozyme, second step of self-splicing, conformation 4, rna
• Biological source: Tetrahymena thermophila; More
• Total number of polymer chains: 3
• Total formula weight: 131448.42

Authors

Li, S.,Michael, Z.P.,Zhang, X.,Greg, P.,Zhang, K. (deposition date: 2022-07-11, release date: 2023-03-29, Last modification date: 2024-07-03)

Primary citation

Li, S.,Palo, M.Z.,Zhang, X.,Pintilie, G.,Zhang, K.
Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM.
Nat Commun, 14:1294-1294, 2023

PubMed Abstract: Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self-splicing reactions, we determine the structures of L-16 Tetrahymena ribozyme in complex with a 5'-splice site analog product and a 3'-splice site analog substrate using cryo-EM. We solve six conformations from a single specimen, corresponding to different splicing intermediates after the first ester-transfer reaction. The structures reveal dynamics during self-splicing, including large conformational changes of the internal guide sequence and the J5/4 junction as well as subtle rearrangements of active-site metals and the hydrogen bond formed between the 2'-OH group of A261 and the N2 group of guanosine substrate. These results help complete a detailed structural and mechanistic view of this paradigmatic group I intron undergoing the second step of self-splicing.

PubMed: 36928031
DOI: 10.1038/s41467-023-36724-5

Experimental method

ELECTRON MICROSCOPY (2.65 Å)