Breaking barriers: Transitioning from X-ray crystallography to cryo-EM for structural studies

Cryo-electron microscopy (cryo-EM) has transformed structural biology by enabling near-atomic resolution of large macromolecular complexes without the need for crystallization. Here, we describe our laboratory's transition from X-ray crystallography to single-particle cryo-EM to investigate the ATPase family AAA+ domain-containing protein 2B (ATAD2B), a chromatin regulator implicated in epigenetic signaling. We outline the challenges encountered during protein expression, purification and sample preparation, including co-purification of the chaperonin GroEL, and the strategies employed to overcome these obstacles. Our workflow highlights critical steps in sample optimization, grid vitrification and data processing using CryoSPARC, cisTEM and Topaz, as well as computational requirements for high-resolution reconstructions. We also discuss model-building, refinement and validation approaches, emphasizing best practices for new cryo-EM users. This work provides practical insights for structural biologists adopting cryo-EM, particularly for large, flexible protein complexes, and underscores the importance of integrated approaches combining biochemical, computational and imaging strategies.