Recent advances in cryo-electron microscopy revolutionized the possibilities and capabilities of structural analysis. This presents an exciting opportunity to explore the architecture of macromolecular-complexes which could not be crystallized, but also opens a window into in situ structural determination. Here, I will discuss the excitement in resolving macromolecular structures at atomic resolution and report on advances and challenges in studying molecular assemblies in individual cells and multicellular organisms at ~1nm of resolution. A special focus will be given to the functional organization of the cell’s cytoskeleton, i.e., the actin cytoskeleton, intermediate filaments and nuclear lamins. Our study indicates that in situ structural biology, at high-resolution, shed light on structural assemblies that can only be studied in their native environment, i.e. the cell.