Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly for chromophore supramolecular aggregates, high-resolution structures are necessary for understanding and modulating the long-range excitonic coupling. Here, we present a 3.3 Å structure of prototypical biomimetic light-harvesting nanotubes derived from an amphiphilic cyanine dye (C8S3-Cl). Helical 3D reconstruction directly visualizes the chromophore packing that controls the excitonic properties. Our structure clearly shows a brick layer arrangement, revising the previously hypothesized herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif—interlocking sulfonates—that may be responsible for the slip-stacked packing and J-aggregate nature of the light-harvesting nanotubes. This work shows how independently obtained native-state structures complement photophysical measurements and will enable accurate understanding of (excitonic) structure–function properties, informing materials design for light-harvesting chromophore aggregates.

冷冻电子显微镜为生物自组装带来了分辨率革命，但合成超分子材料仅解析了少数结构。特别是对于发色团超分子聚集体，高分辨率结构对于理解和调节长程激子耦合是必要的。在这里，我们提出了一种源自两亲性花青染料 (C8S3-Cl) 的原型仿生光捕获纳米管的 3.3 Å 结构。螺旋 3D 重建直接可视化控制激子特性的发色团堆积。我们的结构清楚地显示了砖层排列，修改了之前假设的人字形排列。此外，我们还发现了一种新的非生物超分子基序——联锁磺酸盐——它可能是造成光捕获纳米管的滑堆积堆积和 J 聚集性质的原因。这项工作展示了独立获得的本征结构如何补充光物理测量，并将能够准确理解（激子）结构功能特性，为光捕获发色团聚集体的材料设计提供信息。