Function-oriented design of supramolecular self-assemblies represents a foundational goal in chemistry. Especially, chromophore self-assemblies display extreme photophysical changes from their monomers that are sensitive to the nanoscale molecular arrangements. Slip-stacked arrangements in J-aggregates lead to red shifts (>200 nm) and enhanced quantum yields. Actively introducing specific molecular arrangements using supramolecular chemistry provides a platform to tune the excitonic couplings and avail exotic photophysical properties. However, the nanoscale molecular arrangements have not yet been directly observed in these solution-state assemblies. Here, we present a high-resolution structure of the prototypical biomimetic light harvesting nanotubes (LHNs) of an amphiphilic cyanine dye (C8S3-Cl). We achieve a 3.3 Å resolution with helical reconstruction of cryo-EM images, directly visualizing the atomic scale parameters and packing arrangements that control the excitonic properties. Our structure clearly shows a brick layer arrangement of the molecules as opposed to the previously thought herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif – interlocking sulfonates, that may be responsible for the slip-stacked packing and ultimately the J-aggregate nature of LHNs. This motif may be relevant towards other amphiphilic self-assemblies, in general and provides a new chemical handle on predictable self-assemblies.