Fig. 6: Topological structures of the RRE RNA conformers.

a, Five RRE molecules in five distinct conformational states, C0–C4, captured by AFM (top), and their recapitulated structures (bottom). The raw single-molecule images were taken once, thus without signal averaging. The red and blue coloured regions indicate the locations of the IIB and IA Rev-binding sites. See also Supplementary Videos 1–5. Scale bar, 10 nm. b, Violin plots showing the estimated accuracy by HORNET for each of the five conformers (Extended Data Fig. 10a) with minimum values of 3.0, 4.3, 3.1, 3.7, 3.0 Å; maximum values of 10.4, 9.4, 8.1,9.2 and 9.7 Å; mean values of 6.9, 7.5, 4.8, 5.4, 6.9 Å; and n = 2,809,043, 1,242,907, 1,389,161, 2,101,611 and 1,388,409 structural models for C0, C1, C2, C3 and C4, respectively c, r.m.s.f. versus residue among the five conformers (left) and the 3D model (C0) in molecular surface superimposed with ribbon diagram (middle), and the RRE secondary structure (right). The residue regions with variations above 10 Å (r.m.s.f. plot, dotted line) are coloured accordingly. d, Distance variation between the two known Rev-binding sites, IIB and IA, for each conformer. e, Design scheme of a branched peptide (top left), with single-bond lysine linkage, offering flexibility to adapt to the conformationally heterogeneous RRE (bottom left), and the end-to-end distance distribution between the two parallel ARMs simulated by a 3.0-μs molecular dynamics calculation (right). f, Electrophoretic mobility shift assay of branched peptide–RRE complexes. Lanes 1, 5 and 10: RRE; The ratios of RRE:peptide:Rev:RibA71 in lanes 2–4 and 6–9 are: 1:4:4:0, 1:4:8:0, 1:16:0 and 1:4:32:0, 1:4:64:0, 1:4:32:150 and 1:4:64:150, respectively. RibA71 comprises three duplexes, and is an adenine riboswitch RNA used as non-specific RNA competing with RRE for peptide binding. The feint and smeared bands in lanes 6–9 are oligomeric Rev–RRE complexes. Gel source data are shown in Supplementary Fig. 1.