8KCB

Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2

Summary for 8KCB

• Entry DOI: 10.2210/pdb8kcb/pdb
• EMDB information: 37098
• Descriptor: Histone H2B.10, Histone H3.1, Histone H4, ... (9 entities in total)
• Functional Keywords: ddm1, nucleosome, h2a, structural protein
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 11
• Total formula weight: 304586.46

Authors

Zhang, H.,Zhang, Y. (deposition date: 2023-08-07, release date: 2024-06-26, Last modification date: 2024-08-21)

Primary citation

Zhang, H.,Gu, Z.,Zeng, Y.,Zhang, Y.
Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures.
Structure, 32:1222-1230.e4, 2024

PubMed Abstract: The SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we determined the cryo-EM structures of DDM1-nucleosome and DDM1-nucleosome complexes at near-atomic resolution in the presence of the ATP analog ADP-BeFx. The structures show that nucleosomal DNA is unwrapped more on the surface of the histone octamer containing histone H2A than that containing histone H2A.W. DDM1 embraces one DNA gyre of the nucleosome and interacts with the N-terminal tails of histone H4. Although we did not observe DDM1-H2A.W interactions in our structures, the results of the pull-down experiments suggest a direct interaction between DDM1 and the core region of histone H2A.W. Our work provides mechanistic insights into the heterochromatin remodeling process driven by DDM1 in plants.

PubMed: 38870940
DOI: 10.1016/j.str.2024.05.013

Experimental method

ELECTRON MICROSCOPY (3.17 Å)