Abstract

Multi-protein complexes are necessary for nearly all cellular processes, and understanding their structure is required for elucidating their function. Current high-resolution strategies in structural biology are effective, but lag behind other fields (e.g. genomics and proteomics) due to their reliance on purified samples rather than characterizing heterogeneous mixtures. Here, we present a method combining single particle analysis by electron microscopy with protein identification by mass spectrometry to structurally characterize macromolecular complexes from extracts of human cells. We obtain three-dimensional structures of native proteasomes directly from ab initio classification of a heterogeneous mixture of protein complexes. In addition, we find an ~1 MDa size structure of unknown composition and reference our proteomics data to suggest possible identities. Our study shows the power of using a shotgun approach to electron microscopy (shotgun EM) when coupled with mass spectrometry as a tool to uncover the structures of macromolecular machines in parallel.