Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Topological crossing in the misfolded ribozyme resolved by cryo-EM.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 119, Issue 37, Page e2209146119, Year 2022
Publish date	Sep 13, 2022
Authors	Shanshan Li / Michael Z Palo / Grigore Pintilie / Xiaojing Zhang / Zhaoming Su / Kalli Kappel / Wah Chiu / Kaiming Zhang / Rhiju Das /
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 ...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.
External links	Proc Natl Acad Sci U S A / PubMed:36067294 / PubMed Central
Methods	EM (single particle)
Resolution	3.01 - 4.01 Å
Structure data	33425 7xsk EMDB-33425, PDB-7xsk: Misfolded Tetrahymena ribozyme conformation 1 Method: EM (single particle) / Resolution: 3.53 Å 33426 7xsl EMDB-33426, PDB-7xsl: Misfolded Tetrahymena ribozyme conformation 2 Method: EM (single particle) / Resolution: 3.84 Å 33427 7xsm EMDB-33427, PDB-7xsm: Misfolded Tetrahymena ribozyme conformation 3 Method: EM (single particle) / Resolution: 4.01 Å 33428 7xsn EMDB-33428, PDB-7xsn: Native Tetrahymena ribozyme conformation Method: EM (single particle) / Resolution: 3.01 Å
Source	tetrahymena thermophila (eukaryote)
Keywords	RNA / Misfolded Tetrahymena Ribozyme / Topological Crossing / Cryo-EM / refolding