9KQ2

Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome

Summary for 9KQ2

• Entry DOI: 10.2210/pdb9kq2/pdb
• EMDB information: 62494
• Descriptor: Histone H3, Histone H4, Histone H2A, ... (8 entities in total)
• Functional Keywords: dna repair, histone ubiquitination, nucleosome, e3 ubiquitin-protein ligase, rnf168, dna binding protein/dna, dna binding protein-dna complex
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 11
• Total formula weight: 210822.63

Authors

Zhu, H.Q. (deposition date: 2024-11-25, release date: 2025-11-12)

Primary citation

Yang, X.,Zhu, H.,Shi, L.,Song, T.,Gong, W.,He, S.,Shan, S.,Xu, C.,Zhou, Z.
AlphaFold-guided structural analyses of nucleosome binding proteins.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: The nucleosome, as the fundamental unit of chromatin, interacts with a diverse range of proteins, crucially regulating gene expression. In this study, we introduce an AlphaFold-based algorithm designed to analyze nucleosome-binding proteins from a dataset of over 7600 human nuclear proteins. Using proteins that interact with the nucleosome acidic patch as a benchmark, our screening achieves a successful prediction rate of 77% (23 out of 30 proteins). This predictive approach has led to the identification of ARID4A and ARID4B as novel nucleosome-binding proteins. Additionally, this analytical method was used to study RING-family ubiquitin E3 ligase RNF168, demonstrating that RNF168 dimerization enhances its binding to the nucleosome, a finding confirmed by cryogenic-electron microscopy structural analysis. Our findings offer a rapid and effective method for the discovery and characterization of nucleosome-binding proteins and emphasize the significant role of ubiquitin E3 ligase dimerization in epigenetic regulation.

PubMed: 40794873
DOI: 10.1093/nar/gkaf735

Experimental method

ELECTRON MICROSCOPY (3.9 Å)