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Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking

Author

Listed:
  • Un Seng Chio

    (University of California San Francisco)

  • Eugene Palovcak

    (University of California San Francisco)

  • Anton A. A. Smith

    (Stanford University
    Technical University of Denmark)

  • Henriette Autzen

    (University of California San Francisco
    University of Copenhagen)

  • Elise N. Muñoz

    (University of California, San Francisco)

  • Zanlin Yu

    (University of California San Francisco)

  • Feng Wang

    (University of California San Francisco)

  • David A. Agard

    (University of California San Francisco)

  • Jean-Paul Armache

    (Pennsylvania State University)

  • Geeta J. Narlikar

    (University of California San Francisco)

  • Yifan Cheng

    (University of California San Francisco
    University of California San Francisco)

Abstract

Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and inconsistent due to complex denaturation at the air-water interface (AWI). Here, to address this issue, we develop graphene-oxide-coated EM grids functionalized with either single-stranded DNA (ssDNA) or thiol-poly(acrylic acid-co-styrene) (TAASTY) co-polymer. These grids protect complexes between the chromatin remodeler SNF2h and nucleosomes from the AWI and facilitate collection of high-quality micrographs of intact SNF2h-nucleosome complexes in the absence of crosslinking. The data yields maps ranging from 2.3 to 3 Å in resolution. 3D variability analysis reveals nucleotide-state linked conformational changes in SNF2h bound to a nucleosome. In addition, the analysis provides structural evidence for asymmetric coordination between two SNF2h protomers acting on the same nucleosome. We envision these grids will enable similar detailed structural analyses for other enzyme-nucleosome complexes and possibly other protein-nucleic acid complexes in general.

Suggested Citation

  • Un Seng Chio & Eugene Palovcak & Anton A. A. Smith & Henriette Autzen & Elise N. Muñoz & Zanlin Yu & Feng Wang & David A. Agard & Jean-Paul Armache & Geeta J. Narlikar & Yifan Cheng, 2024. "Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46178-y
    DOI: 10.1038/s41467-024-46178-y
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    References listed on IDEAS

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