8SN3

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1)

Summary for 8SN3

• Entry DOI: 10.2210/pdb8sn3/pdb
• EMDB information: 40611
• Descriptor: Histone H3.1, ZINC ION, Histone H4, ... (10 entities in total)
• Functional Keywords: nucleosome core particle, chromatin, rnf168, ring domain, ubch5c, dna repair, dna double-strand break, homologous recombination, 53bp1, ubiquitin, structural protein-dna-transferase complex, transferase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 13
• Total formula weight: 238148.07

Authors

Hu, Q.,Botuyan, M.V.,Zhao, D.,Cui, G.,Mer, G. (deposition date: 2023-04-26, release date: 2024-01-17, Last modification date: 2024-10-23)

Primary citation

Hu, Q.,Zhao, D.,Cui, G.,Bhandari, J.,Thompson, J.R.,Botuyan, M.V.,Mer, G.
Mechanisms of RNF168 nucleosome recognition and ubiquitylation.
Mol.Cell, 84:839-853.e12, 2024

PubMed Abstract: RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation.

PubMed: 38242129
DOI: 10.1016/j.molcel.2023.12.036

Experimental method

ELECTRON MICROSCOPY (3.8 Å)