EMD-33811

Single-particle
2.97 Å
EMD-33811 Deposition: 11/07/2022
Map released: 29/03/2023
Last modified: 03/07/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-33811

Cryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicing

EMD-33811

Single-particle
2.97 Å
EMD-33811 Deposition: 11/07/2022
Map released: 29/03/2023
Last modified: 03/07/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Tetrahymena
Sample: Cryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicing
Fitted models: 7yg8 (Avg. Q-score: 0.419)

Deposition Authors: Li S, Michael ZP, Zhang X, Greg P, Zhang K , Zhang K , Liu L
Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM.
Li S, Palo MZ , Zhang X, Pintilie G , Zhang K
(2023) Nat Commun , 14 , 1294 - 1294
PUBMED: 36928031
DOI: doi:10.1038/s41467-023-36724-5
ISSN: 2041-1723
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.