Low-Energy Polishing Facilitates Breaking the Resolution Barrier of In Situ Cryo-EM

Abstract In situ structural analysis allows direct visualization of protein structures in their native cellular environments, but near-atomic resolution in cellular lamellae has been significantly limited to exceptionally large complexes such as ribosomes. A key factor underlying this limitation is the degradation of data quality of thin lamellae caused by substantial subsurface damage from cryo-focused ion beam (cryo-FIB). Here, we developed a cryogenic low-energy polishing in FIB approach, which reliably produces thin lamellae with low damage across different cell types. This advance, combined with in situ single particles analysis, has pushed down the molecular weight lower limit for in situ reconstruction at near-atomic resolution to ∼400 kDa. We demonstrate this by resolving photosynthetic complexes (3.4 Å and 3.3 Å), metabolic enzymes (3.3 Å), chloroplast ribosome (4.0 Å) and respiratory chain complexes (3.7 Å) from Chlamydomonas reinhardtii . Furthermore, the efficient workflow enables rapid structural feedback upon changes in cellular states, offering a practical way to perform multi-condition in situ structural analysis.