7XSL

Misfolded Tetrahymena ribozyme conformation 2

Summary for 7XSL

• Entry DOI: 10.2210/pdb7xsl/pdb
• EMDB information: 33426
• Descriptor: RNA (388-MER) (1 entity in total)
• Functional Keywords: misfolded tetrahymena ribozyme, topological crossing, cryo-em, refolding, rna
• Biological source: Tetrahymena thermophila
• Total number of polymer chains: 1
• Total formula weight: 125402.95

Authors

Li, S.,Palo, M.,Pintilie, G.,Zhang, X.,Su, Z.,Kappel, K.,Chiu, W.,Zhang, K.,Das, R. (deposition date: 2022-05-14, release date: 2022-08-03, Last modification date: 2024-07-03)

Primary citation

Li, S.,Palo, M.Z.,Pintilie, G.,Zhang, X.,Su, Z.,Kappel, K.,Chiu, W.,Zhang, K.,Das, R.
Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM.
Proc.Natl.Acad.Sci.USA, 119:e2209146119-e2209146119, 2022

PubMed Abstract: The 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) , 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 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.

PubMed: 36067294
DOI: 10.1073/pnas.2209146119

Experimental method

ELECTRON MICROSCOPY (3.84 Å)