Abstract

Most structural biology focuses on the structure and function of individual macromolecular complexes, but falls short of revealing how they come together to give rise to cellular functions. As a consequence, structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Here, cryo-electron tomography (cryo-ET) provides a unique opportunity for obtaining structural information across a wide range of spatial scales – from whole cells to individual macromolecules. We develop and employ advanced sample preparation techniques for in-cell cryo-electron tomography, including cryo-focused ion beam thinning guided by 3D correlative fluorescence microscopy. Preparations of site-specific ‘electron-transparent windows’ in cellular model systems enable assignment of molecular structures directly from three-dimensional stills of intact cells and reveal their molecular sociology. Using the genome-reduced human pathogen Mycoplasma pneumoniae as a model system, we further developed the synergistic application of whole-cell crosslinking mass spectrometry, cellular cryo-ET and integrative modelling, and determine in-cell structures of transient, actively transcribing RNA polymerases coupled to a translating ribosomes. Recent computational breakthroughs now allow resolving these molecular machines to residue-level and reveal small molecule antibiotics bound to their active cite within the intact pathogen. These methodologies unlock an enormous potential for novel discovery enabled by label-free structural cell biology.