LORA

A dataset of long-range RNA 3D modules

Reference

D.R. Bohdan, V.V. Voronina, J.M. Bujnicki, E.F. Baulin (2023) A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures. Nucleic Acids Research. gkad605. DOI: 10.1093/nar/gkad605

Check out our other developments

Content

data

The coordinate files from PDB (Berman et al. 2000) and their annotations of the RNA interactions used in this work.

• cif_files_part1.zip & cif_files_part2.zip - Coordinate files in mmCIF format
• pdb_files.zip - Coordinate files in PDB format
• clarna.zip - ClaRNA annotations (Waleń et al. 2014)
• dssr.zip - DSSR annotations (Lu et al. 2015)
• fr3d.zip - FR3D annotations (Sarver et al. 2008)
• mc-annotate.zip - MC-Annotate annotations (Gendron et al. 2001)
• rnaview.zip - RNAView annotations (Yang et al. 2003)

Table S1

The non-redundant list of 97 RNA chains used in this work.

Table S2

The table of 17,272 long-range nucleotide doublets. For each doublet, the annotations of interactions and motif types are provided. Each doublet is assigned to a LORA module.

Table S3

The table of 180 long-range doublets annotated with different Leontis-Westhof base pair types by different tools.

Table S4

The table of 35 D-loop/T-loop-like motifs.

Table S5

The table of 45 long-range tertiary motifs.

Table S6

The table of 3880 long-range tertiary motif matches in the LORA modules.

Table S7

The table of 515 long-range doublets matching the cSS base pair motif (motif 1).

Table S8

The table of 1,264 LORA modules annotated with their descriptive types and involved interactions andd motifs.

Table S9

The table of 17 RINs and 24 LORA modules from the intersection in PDB entries between LORA and CaRNAval database (Reinharz et al. 2018).

modules

The dataset of 1,264 long-range RNA 3D modules (LORA modules). Each module is identified with its PDB entry and an ordinal number, e.g. 2z75_3. All LORA modules are present in both mmCIF and PDB formats.

motifs

The data on the long-range motif instances and motifs derived from the LORA modules. Motif instances are named using their source LORA module and an ordinal number, e.g. 2z75_1_259.

• motifs.zip - the table listing the residues of all the derived 489,999 motif instances.
• clusters - intermediate clusters of the motif instances from 2 to 20 residues in size. All cluster members are present in PDB format. Cluster centers are present in PDB and mmCIF formats.
• library - the derived 45 long-range RNA tertiary motifs. All the motifs are present in both mmCIF and PDB formats.
• matches - the derived 3880 long-range RNA tertiary motif matches in the LORA modules. All the motif matches are present in both mmCIF and PDB formats.