8VHK

NPM2-H1.8 isolated from Xenopus egg extract (Stretched form)

Summary for 8VHK

• Entry DOI: 10.2210/pdb8vhk/pdb
• EMDB information: 43240
• Descriptor: Nucleoplasmin isoform X1 (1 entity in total)
• Functional Keywords: h1, xenopus egg extract, magic-cryo-em, histone chaperone, chaperone
• Biological source: Xenopus laevis (African clawed frog)
• Total number of polymer chains: 5
• Total formula weight: 109747.34

Authors

Arimura, Y.,Funabiki, H. (deposition date: 2024-01-02, release date: 2024-12-11, Last modification date: 2025-06-04)

Primary citation

Arimura, Y.,Konishi, H.A.,Funabiki, H.
MagIC-Cryo-EM, structural determination on magnetic beads for scarce macromolecules in heterogeneous samples.
Elife, 13:-, 2025

PubMed Abstract: Cryo-EM single-particle analyses typically require target macromolecule concentration at 0.05~5.0 mg/ml, which is often difficult to achieve. Here, we devise netic solation and oncentration (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 the linker histone H1.8-associated nucleosomes that were isolated from interphase and metaphase chromosomes in egg extract. Combining plicated election o xclude ubbish particles (DuSTER), a particle curation method that excludes low signal-to-noise ratio particles, we also resolved the 3D cryo-EM structures of nucleoplasmin NPM2 co-isolated with the linker histone H1.8 and revealed distinct open and closed structural variants. Our study demonstrates the utility of MagIC-cryo-EM for structural analysis of scarce macromolecules in heterogeneous samples and provides structural insights into the cell cycle-regulation of H1.8 association to nucleosomes.

PubMed: 40390365
DOI: 10.7554/eLife.103486

Experimental method

ELECTRON MICROSCOPY (5.16 Å)