8V6V

Cryo-EM structure of doubly-bound SNF2h-nucleosome complex

Summary for 8V6V

• Entry DOI: 10.2210/pdb8v6v/pdb
• Related: 8V4Y
• EMDB information: 42977 43000 43001 43002
• Descriptor: Histone H3.2, Histone H4, Histone H2A type 1, ... (9 entities in total)
• Functional Keywords: nucleosome, chromatin remodeler, iswi, snf2h, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 12
• Total formula weight: 480985.23

Authors

Chio, U.S.,Palovcak, E.,Armache, J.P.,Narlikar, G.J.,Cheng, Y. (deposition date: 2023-12-03, release date: 2024-03-20)

Primary citation

Chio, U.S.,Palovcak, E.,Smith, A.A.A.,Autzen, H.,Munoz, E.N.,Yu, Z.,Wang, F.,Agard, D.A.,Armache, J.P.,Narlikar, G.J.,Cheng, Y.
Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking.
Nat Commun, 15:2225-2225, 2024

PubMed 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.

PubMed: 38472177
DOI: 10.1038/s41467-024-46178-y

Experimental method

ELECTRON MICROSCOPY (2.8 Å)