Figure 3. Structural analysis of ^βCDRhuA-^azoRhuA nanotubes.

(A) A representative cryo-EM image of co-assembled ^βCDRhuA-^azoRhuA nanotubes, showing variations in the tube diameters.

(B) Distribution of ^βCDRhuA-^azoRhuA nanotubes with different diameters, determined from cryoEM (top) and SAXS (bottom) measurements (see Methods for details).

(C) Left and middle panels: Cryo-EM helical reconstructions of co-assembled RhuA nanotubes of different diameters shown from the side and the top. Right panels: Helical nets of the corresponding nanotubes. The convention used is that the surface of the tube is unrolled and is being viewed from the outside surface of the nanotube. The positions of the dots correspond to the helical arrangement of the asymmetric units composed of a pair of two neighboring ^βCDRhuA and ^azoRhuA units. The three reconstructed tubes are generated from 10, 11, 12 protofilaments with a right-handed twist (dashed lines) in the absence of rotational point group symmetry (C₁ symmetry) or C₃ symmetry (the bottom one only).

(D) Structural model of tetrameric RhuA monomers fitted into the EM volume map of the 52-nm-diameter nanotubes, indicating that the neighboring RhuA units adopt an alternating arrangement. Position 98 of RhuA is highlighted in black.

(E) Density maps obtained from the single-particle reconstruction of a focused region on the nanotubes. Even without the applied helical symmetry, the density belonging to the host-guest pairs still maintains a pseudo-C₂ symmetry, indicating the formation of a “dimer-of-dimers” host-guest pair. The pairwise distances between C98 residues are indicated in the right panel.