Natural hybrid silica/protein superstructure at atomic resolution
Significance Using hybrid silica/protein templates, nature has mastered the fabrication of extremely complex macroscopic glass assemblies. Highly symmetric skeletal elements in demosponges are formed following a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by highly ordered proteinaceous filaments. Here we provide a comprehensive three-dimensional atomistic view of this hybrid assembly. The structure, occurring in the crystalline form in vivo, was measured in situ using the serial crystallography method. Together with a high-resolution transmission electron microscopy and energy-dispersive X-ray spectroscopy study, we provide structural, chemical, and functional information on a naturally forming hybrid mineral/organic crystal. Formation of highly symmetric skeletal elements in demosponges, called spicules, follows a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by a highly ordered proteinaceous scaffold, the axial filament. The enzymatically active proteins, silicateins, are assembled into a slender hybrid silica/protein crystalline superstructure that directs the morphogenesis of the spicules. Furthermore, silicateins are known to catalyze the formation of a large variety of other technologically relevant organic and inorganic materials. However, despite the biological and biotechnological importance of this macromolecule, its tertiary structure was never determined. Here we report the atomic structure of silicatein and the entire mineral/organic hybrid assembly with a resolution of 2.4 Å. In this work, the serial X-ray crystallography method was successfully adopted to probe the 2-µm-thick filaments in situ, being embedded inside the skeletal elements. In combination with imaging and chemical analysis using high-resolution transmission electron microscopy, we provide detailed information on the enzymatic activity of silicatein, its crystallization, and the emergence of a functional three-dimensional silica/protein superstructure in vivo. Ultimately, we describe a naturally occurring mineral/protein crystalline assembly at atomic resolution.