Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM.

Shanshan Li, Michael Z Palo, Grigore Pintilie, Xiaojing Zhang, Zhaoming Su, Kalli Kappel, Wah Chiu, Kaiming Zhang, Rhiju Das

Proceedings of the National Academy of Sciences of the United States of America 2022 Sep 13

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The Tetrahymena group I intron has been a key system in the understanding of RNA folding and misfolding. The molecule folds into a long-lived misfolded intermediate (M) in vitro, which has been known to form extensive native-like secondary and tertiary structures but is separated by an unknown kinetic barrier from the native state (N). Here, we used cryogenic electron microscopy (cryo-EM) to resolve misfolded structures of the Tetrahymena L-21 ScaI ribozyme. Maps of three M substates (M1, M2, M3) and one N state were achieved from a single specimen with overall resolutions of 3.5 Å, 3.8 Å, 4.0 Å, and 3.0 Å, respectively. Comparisons of the structures reveal that all the M substates are highly similar to N, except for rotation of a core helix P7 that harbors the ribozyme's guanosine binding site and the crossing of the strands J7/3 and J8/7 that connect P7 to the other elements in the ribozyme core. This topological difference between the M substates and N state explains the failure of 5'-splice site substrate docking in M, supports a topological isomer model for the slow refolding of M to N due to a trapped strand crossing, and suggests pathways for M-to-N refolding.

Citation

Shanshan Li, Michael Z Palo, Grigore Pintilie, Xiaojing Zhang, Zhaoming Su, Kalli Kappel, Wah Chiu, Kaiming Zhang, Rhiju Das. Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM. Proceedings of the National Academy of Sciences of the United States of America. 2022 Sep 13;119(37):e2209146119