SNAP output for PDB entry 8whb [SNAP web server]

PDB-id

8whb; SNAP-derived features in text and JSON formats; DNAproDB

Class

gene regulation

Method

cryo-EM (3.17 Å)

Summary

Structure of nucleosome core particle of arabidopsis thaliana

Reference

Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J (2024): "Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation." Nat.Plants, 10, 374-380. doi: 10.1038/s41477-024-01640-z.

Abstract

Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers₁. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components_2-5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation_6-11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeF_x-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeF_x-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.