EMD-34028

Single-particle
3.38 Å
EMD-34028 Deposition: 07/08/2022
Map released: 17/08/2022
Last modified: 03/07/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-34028

cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1

EMD-34028

Single-particle
3.38 Å
EMD-34028 Deposition: 07/08/2022
Map released: 17/08/2022
Last modified: 03/07/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Homo sapiens, synthetic construct
Sample: Complex of 53BP1(1484-1972) and gammaH2AXK15ub-H4K20me2 nucleosome
Fitted models: 7yqk (Avg. Q-score: 0.424)

Deposition Authors: Ai HS , GuoChao C, Qingyue G, Ze-Bin T, Zhiheng D, Xin L, Fan Y, Ziyu X, Jia-Bin L , Changlin T , Liu L
Chemical Synthesis of Post-Translationally Modified H2AX Reveals Redundancy in Interplay between Histone Phosphorylation, Ubiquitination, and Methylation on the Binding of 53BP1 with Nucleosomes.
Ai H , Chu GC, Gong Q, Tong ZB, Deng Z, Liu X, Yang F, Xu Z, Li JB , Tian C, Liu L
(2022) J Am Chem Soc , 144 , 18329 - 18337
PUBMED: 36166692
DOI: doi:10.1021/jacs.2c06156
ISSN: 1520-5126
ASTM: JACSAT
Abstract:
The chemical synthesis of homogeneously modified histones is a powerful approach to quantitatively decipher how post-translational modifications (PTMs) modulate epigenetic events. Herein, we describe the expedient syntheses of a selection of phosphorylated and ubiquitinated H2AX proteins in a strategy integrating expressed protein hydrazinolysis and auxiliary-mediated protein ligation. These modified H2AX proteins were then used to discover that although H2AXS139 phosphorylation can enhance the binding of the DNA damage repair factor 53BP1 to either an unmodified nucleosome or that bearing a single H2AXK15ub or H4K20me2 modification, it augments 53BP1's binding only weakly to nucleosomes bearing both H2AXK15ub and H4K20me2. To better understand why such a trivalent additive effect is lacking, we solved the cryo-EM structure (3.38 Å) of the complex of 53BP1 with the H2AXK15ub/S139ph_H4K20me2 nucleosome, which showed that H2AXS139 phosphorylation distorts the interaction interface between ubiquitin and 53BP1's UDR motif. Our study revealed that there is redundancy in the interplay of multiple histone PTMs, which may be useful for controlling the dynamic distribution of effector proteins onto nucleosomes bearing different histone variants and PTMs in a time-dependent fashion, through specific cellular biochemical events.