9R5K

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

Summary for 9R5K

• Entry DOI: 10.2210/pdb9r5k/pdb
• EMDB information: 53590
• 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: 209566.88

Authors

Sundaramoorthy, R.,Hughes, A.,Owen-hughes, T.A. (deposition date: 2025-05-09, release date: 2026-01-28)

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 nascent exit linker to approximately 15bp, 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 (4.2 Å)