The yeast nuclear pore complex (NPC) is an organelle-sized macromolecular assembly (> 500 proteins) that plays key roles in the nuclear-cytoplasmic transport of numerous biomolecules. Approximately one-third of NPC proteins contain intrinsically disordered regions that populate the NPC central channel and, through interaction with cargo-carrying transport factors, mediate transport. The sheer size, complexity, and flexibility of the NPC are among the main challenges for a detailed structural characterization of the complex. Shi and colleagues have developed novel hybrid structural approaches that integrate a large body of proteomic data generated by cutting-edge mass spectrometry (MS) technologies to study the endogenous NPC. These approaches include affinity isolation/MS, chemical cross-linking/MS, and native MS, together with other structural information—from cryo-EM, X-ray crystallography, and small angle X-ray scattering—as well as hybrid modeling methods. They have thus unraveled the complete structure of the yeast NPC at subnanometer precision. Their work uncovers the detailed architecture of this basic, conserved, and essential eukaryotic machinery that has been associated with many cancers and viral diseases in humans. The novel hybrid approaches, including those proteomic tools that they have developed, will find utilities in solving the structures of many other huge, flexible, and dynamic macromolecular assemblies in the cell.