9R5W

Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.

Summary for 9R5W

• Entry DOI: 10.2210/pdb9r5w/pdb
• EMDB information: 53596
• Descriptor: DNA (162-MER), Histone H3.2, Histone H4, ... (6 entities in total)
• Functional Keywords: nucleosome, remodelling enzyme, gene regulation
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 10
• Total formula weight: 209551.87

Authors

Sundaramoorthy, R.,Hughes, A.,Owen-hughes, T.A. (deposition date: 2025-05-10, release date: 2026-02-04)

Primary citation

Hughes, A.L.,Sundaramoorthy, R.,Owen-Hughes, T.
Structural characterisation of chromatin remodelling intermediates supports linker DNA-dependent product inhibition as a mechanism for nucleosome spacing.
Elife, 14:-, 2025

PubMed Abstract: Previously, we showed that Chd1 chromatin remodelling enzyme associates with nucleosomes oriented towards the longer linker (Sundaramoorthy et al., 2018) (1). Here, we report a series of structures of Chd1 bound to nucleosomes during ongoing ATP-dependent repositioning. Combining these with biochemical experiments and existing literature, we propose a model in which Chd1 first associates oriented to sample putative entry DNA. In an ATP-dependent reaction, the enzyme then redistributes to the opposite side of the nucleosome, where it subsequently adopts a conformation productive for DNA translocation. Once this active complex extends the nascent exit linker to approximately 15 bp, it is sensed by the Chd1 DNA binding domain, resulting in conversion to a product-inhibited state. These observations provide a mechanistic basis for the action of a molecular ruler element in nucleosome spacing.

PubMed: 41439750
DOI: 10.7554/eLife.52513

Experimental method

ELECTRON MICROSCOPY (3.8 Å)