Figure 2 | Scientific Reports

Figure 2

From: Structural prerequisites for CRM1-dependent nuclear export signaling peptides: accessibility, adapting conformation, and the stability at the binding site

Figure 2

Location of the NES consensus patterns in Snurportin-1. (A) Disordered propensity, conserved domain information, predicted secondary structure, and the location of the consensus patterns are plotted together. The defined ordered region (by the cutoff value of 0.1; gray dashed line) is represented by the sky-blue box at the top. The regions of the conserved domains annotated in smart, Pfam, NCBI-curated, and CDD are marked in the middle. The predicted secondary structures (SS) were colored by red, black, and blue for α-helix, coil, and β-strand, respectively. The gradient of the color corresponds to the confidence level of the prediction. For the NES regions, experimentally validated regions are displayed in blue (with mutation data annotated in NESdb) and cyan (annotated as a functional sequence in NESdb or as a site in validNES). All the consensus pattern matching segments are located at the bottom. Segments not in the ordered regions and without β-strand predictions in the middle are highlighted in yellow. The red boxes are the pattern-matching segments overlapping with experimental evidence. (B) The crystal structure of CRM1-SNUPN complex structure (PDB id: 3GB8)12. SNUPN is displayed by the cartoon, and the validated NES motif, Snurportin1 domain, and Snurportin-1_C domain are colored in red, green, and orange, respectively. CRM1 is represented by a white surface. (C) The list of the pattern-matching sequences in SNUPN. In the ‘candidates’ column, NES candidates and false positives are annotated with “cand” and “fp,” respectively. If the segment is located in the disordered or boundary region, it is flagged with “_D” while in the ordered region, it is flagged with “_O.” If the segment’s β-strand content is over 0.5, it is flagged with “_beta.” In the ‘sequence’ column, hydrophobic positions are colored in red, and the positions with the experimental evidence are marked with ‘*’ (mutation) and ‘+’ (functional sequence in NESdb or sites in validNES). The values in ‘diso,’ ‘spotd,’ and ‘iup’ are the average disordered propensity for the segment calculated by DISOPRED3, SPOT-Disorder, and IUPRED2A, respectively. The locations with respect to disordered/ordered region or conserved domains are listed in the ‘loc_DISO’ and ‘loc_CDD’ columns. ‘beta’ is for the β-strand content in the middle of the segment.

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