8WHB

Structure of nucleosome core particle of Arabidopsis thaliana

Summary for 8WHB

• Entry DOI: 10.2210/pdb8whb/pdb
• EMDB information: 37538
• Descriptor: Histone H3.1, Histone H4, Histone H2A.6, ... (6 entities in total)
• Functional Keywords: nucleosome, chromatin, histone, protein dna interaction, nucleoprotein, gene regulation
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 10
• Total formula weight: 204535.30

Authors

Liu, Y.,Zhang, Z.,Du, J. (deposition date: 2023-09-23, release date: 2024-04-17, Last modification date: 2025-07-16)

Primary citation

Liu, Y.,Zhang, Z.,Hu, H.,Chen, W.,Zhang, F.,Wang, Q.,Wang, C.,Yan, K.,Du, J.
Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.
Nat.Plants, 10:374-380, 2024

PubMed 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 remodellers. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeF-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-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.

PubMed: 38413824
DOI: 10.1038/s41477-024-01640-z

Experimental method

ELECTRON MICROSCOPY (3.17 Å)