8ZJT

Structure of free nucleosome

Summary for 8ZJT

• Entry DOI: 10.2210/pdb8zjt/pdb
• EMDB information: 60156
• Descriptor: Histone H3.2, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: nucleosome, histone, dna, structural protein/dna, structural protein-dna complex
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 202825.08

Authors

Xu, K.,Zhang, Y.,Yin, Y.,Xue, W.,Han, Y.,Tian, Y. (deposition date: 2024-05-15, release date: 2025-08-13)

Primary citation

Xue, W.,Han, Y.,Tian, Y.,Wang, J.,Xie, Z.,Zheng, X.,Yue, X.,Dong, S.,Li, H.,Luo, Z.,Zhang, S.,Yang, Y.,Zou, Z.,Li, W.,Ma, N.,Zhu, F.,Chen, C.,Yin, Y.,Zhang, Y.,Xu, K.
Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Among the regulatory factor X (RFX) transcription factor family, RFX5 is uniquely reported to bind nucleosomes and induce nucleosome remodeling in vivo. Dysfunctions in RFX5 have been implicated in various diseases. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the RFX5-nucleosome complex, revealing that the extended DNA binding domain (eDBD) of RFX5 binds to the nucleosome at superhelical location +2. RFX5 eDBD engages not only with nucleosomal DNA but also with histones through extensive interactions. Compared to the structure of a free nucleosome, RFX5 eDBD induces localized distortion of the bound DNA gyre and detachment of the adjacent DNA gyre in the RFX5-nucleosome complex. This structural alteration could potentially increase DNA accessibility and enhance transcriptional activity in vivo. Overall, our study provides novel insights into the mechanisms by which RFX5 eDBD interacts with and destabilizes nucleosomes.

PubMed: 40744500
DOI: 10.1093/nar/gkaf734

Experimental method

ELECTRON MICROSCOPY (3.2 Å)