9L22

hDEK-nucleosome complex (conformation 2)

Summary for 9L22

• Entry DOI: 10.2210/pdb9l22/pdb
• EMDB information: 62766
• Descriptor: Histone H3.3, Histone H4, Histone H2A type 1-B/E, ... (8 entities in total)
• Functional Keywords: nucleosome complex, gene regulation
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 12
• Total formula weight: 310888.00

Authors

Liu, Y.,Wang, C.,Huang, H. (deposition date: 2024-12-16, release date: 2025-05-07, Last modification date: 2025-05-28)

Primary citation

Shen, Y.,Liu, Y.,Guo, M.,Mao, S.,Chen, R.,Wang, M.,Li, Z.,Li, Y.,Chen, W.,Chen, F.,Wu, B.,Wang, C.,Chen, W.,Cui, H.,Yuan, K.,Huang, H.
DEK-nucleosome structure shows DEK modulates H3K27me3 and stem cell fate.
Nat.Struct.Mol.Biol., 2025

PubMed Abstract: DEK is a highly conserved chromatin-associated oncoprotein that has important roles in regulating chromatin dynamics and stem cell fate. Dysregulation of DEK is associated with stem cell dysfunction and cancers, including acute myeloid leukemia. Despite its importance in chromatin regulation, the structural mechanisms underlying DEK's interaction with chromatin and its influence on gene regulation remain poorly understood. Here we combined cryogenic electron microscopy (cryo-EM), biochemical and cellular approaches to investigate the molecular mechanisms and functional importance of DEK's interaction with chromatin. Our cryo-EM structures reveal the structural basis of the DEK-nucleosome interaction. Biochemical and cellular results demonstrate that this interaction is crucial for DEK deposition onto chromatin. Furthermore, our results reveal that DEK safeguards mouse embryonic stem cells from acquiring primitive endoderm fates by modulating the repressive histone mark H3K27me3. Together, our study provides crucial molecular insights into the structure and function of DEK, establishing a framework for understanding its roles in chromatin biology and cell fate determination.

PubMed: 40379883
DOI: 10.1038/s41594-025-01559-9

Experimental method

ELECTRON MICROSCOPY (3 Å)