Fig 7. RBM20 RNA recognition motif (RRM)-RNA interaction predicted by AlphaFold 3.

(A): Predicated structure of human RBM20 RRM domain (green) in complex with AUCUUA RNA (brown). The terminals, protein secondary structures and the nucleotides were annotated. The numbers after the nucleotides represented their positions in the fragments. (B): A comparison of the predicted structure in (A) with structure by NMR spectroscopy in mouse—RBM20 RRM domain (pink) and AUCUUA RNA (indigo). The mouse structure was downloaded from Protein Data Bank (PDB) with accession ID 6SO9 and superposed with the predicted structure in (A). The lowest energy structure model of 6SO9 with the lowest root mean square deviation (RMSD)—model 1 and RMSD = 1.54 Å—was presented. The two structures were superposed with the protein chains. (C): The RNA sequence (5’ → 3’) at chr9: 129,915,816−129,916,130 (hg38), containing the target exon (chr9: 129,915,966 − 129,915,980; green) of the skipped exon event at FNBP1 and 150 nucleotides flanking intronic regions at both sides. The corresponding 1-based genome coordinates were labeled above the sequence. The flanking ±20 nucleotides were labeled in grey. The intronic UCUU and UUCU sequences were labeled in yellow. The motifs predicted to be bound by RRM, as in (D) and (E), were underlined with red boxes. AlphaFold 3 predicted the interactions between human RBM20 and fragments of FNBP1 at 5’ intronic region (D) and 3’ intronic region (E) of the target exon, respectively. Only the interaction regions of the RNA fragments were presented.