GNRA

Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures

Reference

J.M. Bujnicki, E.F. Baulin (2025) Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures. Scientific Reports 15.1: 37081. DOI: 10.1038/s41598-025-21072-9

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Content

Figures

Manuscript figures

Variants

The representative matches of the twelve recurrent backbone topology GNRA-tetraloop motif variants in PDB format

highres_filter

The materials when applying 4.0 angstrom resolution threshold for PDB entries

reference_bias

The materials when searching with alternative references (UMAC and UAA/GAN)

files

• 8VTW_CGAAAG.cif - The six-residue reference in mmCIF format
• 8VTW_GAAA.cif - The four-residue reference in mmCIF format
• CGAAAG.artem - Raw ARTEM output for the six-residue reference search
• FigureRMSDthresh.py - Python script to plot RMSD distributions
• GAAA.artem - Raw ARTEM output for the four-residue reference search
• GNRA_pairwise_RMSD.csv - Pairwise RMSD values among six-residue motifs
• GNRA_pairwise_RMSD4.csv - Pairwise RMSD values among four-residue motifs
• HL_85603.2.csv - The GNRA motif class of the RNA 3D Motif Atlas
• README.md - This README file
• REPRODUCE.md - The steps to reproduce the results
• TableS1.xlsx - Table S1. List of 23,283 non-redundant matches of the GNRA motif.
• TableS2.xlsx - Table S2. List of 13,729 unique instances of the GNRA tetraloop motif matches
• TableS3.xlsx - Table S3. List of 59 unique instances of the GNRA tetraloop motif strand topologies
• annotate_hits.py - Python script to annotate ARTEM matches with structural features
• annotated_hits.tsv - The list of annotated matches
• choose_4rmsdmax.py - Python script to select the RMSD thresholds
• choose_GNRA_reference.py - Python script to select the GNRA tetraloop motif reference
• filter_hits.py - Python script to filter redundant matches
• nr_hits.tsv - The list of non-redundant matches
• nr_hits_multichain.tsv - The list of multi-chain matches
• nrlist_3.370_all.csv - The BGSU representative set of RNA structures
• overlap_artem_HL_85603.2.tsv - RNA3DMotifAtlas-ARTEM benchmark data
• pdb_download.py - Python script to download nucleic acid-containing PDB entries
• pdb_process.py - Python script to process the PDB entries
• pdb_resol.py - Python script to retrieve resolutions of the PDB entries
• pdb_resol.tsv - The list of resolutions of the PDB entries
• postprocess_artem.py - Python script to parse ARTEM matches
• processed_hits.tsv - The list of parsed ARTEM matches
• run_DSSR.py - Python script to run DSSR annotations
• stat.ipynb - Jupyter Notebook with summary statistics of the dataset
• unique_hits.tsv - The list of structurally unique matches
• unique_topologies.tsv - The list of unique backbone topology variants of the GNRA tetraloop motif