Structure first – exploration and discovery with cryo-electron microscopy

The ability to directly observe living systems at finer levels of detail is a strong catalyst for biological discovery. This Perspective highlights how cryo-electron microscopy (cryo-EM) is enabling a 'structure-first approach' that can be harnessed for exploration and discovery at the molecular scale, as exemplified in recent studies across the diverse biological contexts curated here. Improvements in throughput, robustness and accessibility of cryo-EM have expanded the range of samples amenable to high-resolution structural analysis to include native protein complexes directly isolated from primary material or imaged unperturbed within the cellular environment. It is therefore increasingly common to encounter unknown proteins in cryo-EM studies, either as unexpected components of a known complex or as completely uncharacterized structures. Advancements in machine learning-assisted model building and protein structure prediction, aided by proteomics and cross-linking mass spectrometry, facilitate protein identification from cryo-EM maps over a wide resolution range, making it possible to derive molecular identity without any prior knowledge or need for specific labelling. In summary, cryo-EM has extended the reach of structural biology beyond focused structure determination of known targets to the exciting frontier of uncovering altogether new proteins and interactions.