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TitleMagIC-Cryo-EM, structural determination on magnetic beads for scarce macromolecules in heterogeneous samples.
Journal, issue, pagesElife, Vol. 13, Year 2025
Publish dateMay 20, 2025
AuthorsYasuhiro Arimura / Hide A Konishi / Hironori Funabiki /
PubMed AbstractCryo-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 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.
External linksElife / PubMed:40390365 / PubMed Central
MethodsEM (single particle)
Resolution5.0 - 5.9 Å
Structure data

43238

8vhi

EMDB-43238, PDB-8vhi:
NPM2-H1.8 isolated from Xenopus egg extract
Method: EM (single particle) / Resolution: 5.0 Å

43239

8vhj

EMDB-43239, PDB-8vhj:
NPM2-H1.8 isolated from Xenopus egg extract (Bent form)
Method: EM (single particle) / Resolution: 5.9 Å

43240

8vhk

EMDB-43240, PDB-8vhk:
NPM2-H1.8 isolated from Xenopus egg extract (Stretched form)
Method: EM (single particle) / Resolution: 5.16 Å

Source
  • xenopus laevis (African clawed frog)
KeywordsCHAPERONE / H1 / Xenopus egg extract / MagIC-cryo-EM / Histone chaperone

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