MagIC-Cryo-EM: Structural determination on magnetic beads for scarce macromolecules in heterogeneous samples.

High-resolution structural reconstitution of biomolecules by cryo-EM single-particle analyses typically demand concentrated samples (0.05~5.0 mg/ml). Here, we introduce Magnetic Isolation and Concentration (MagIC)-cryo-EM, a technique enabling direct structural analysis of targets captured on magnetic beads, thereby reducing the targets' concentration requirement to < 0.0005 mg/ml. Adapting MagIC-cryo-EM to a Chromatin Immunoprecipitation protocol, we characterized structural variations of oocyte-specific linker histone H1.8 associated nucleosomes isolated from interphase and metaphase chromosomes in Xenopus egg extract. Combining Duplicated Selection To Exclude Rubbish particles (DuSTER), a particle curation method that removes low signal-to-noise ratio particles, we also resolved the 3D cryo-EM structures of H1.8-bound nucleoplasmin NPM2 isolated from interphase chromosomes, revealing distinct open and closed structural variants. Our study demonstrates the utility of MagIC-cryo-EM for structural analysis of macromolecules difficult to purify and offers structural insights into the chaperone NPM2 interacts with its targets and the cell cycle-regulation of H1.8 association to nucleosomes.