RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron maps, followed by clustering of the preferred combinations of torsion angles were performed on this dataset. Eighteen non-A-type conformations and 14 A-RNA related conformations were discovered and their torsion angles were determined; their Cartesian coordinates are available.

Center for Complex Molecular Systems and Biomolecules and Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Flemingovo n 2 CZ 16610 Prague Czech Republic

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When will RNA get its AlphaFold moment?

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

A unified dinucleotide alphabet describing both RNA and DNA structures

Automatic workflow for the classification of local DNA conformations

Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods

DNA conformations and their sequence preferences

Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

Molecular dynamics simulations of sarcin-ricin rRNA motif

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PDB
1J5E, 1JJ2