9IPU image
Entry Detail
PDB ID:
9IPU
EMDB ID:
Keywords:
Title:
cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-07-11
Release Date:
2024-10-02
Method Details:
Experimental Method:
Resolution:
4.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Histone H3.2
Chain IDs:B (auth: A), F (auth: E)
Chain Length:135
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H4
Chain IDs:C (auth: B), G (auth: F)
Chain Length:102
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H2A type 1-B/E
Chain IDs:D (auth: C), H (auth: G)
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H2B type 1-K
Chain IDs:E (auth: D), I (auth: H)
Chain Length:125
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H1.0
Chain IDs:A (auth: I)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:DNA (171-MER)
Chain IDs:M (auth: J)
Chain Length:171
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin-conjugating enzyme E2 D3
Chain IDs:J (auth: K)
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:E3 ubiquitin-protein ligase RNF168
Chain IDs:K (auth: L)
Chain Length:193
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin
Chain IDs:L (auth: M)
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:DNA (171-MER)
Chain IDs:N
Chain Length:171
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Promotion of RNF168-Mediated Nucleosomal H2A Ubiquitylation by Structurally Defined K63-Polyubiquitylated Linker Histone H1.
Angew.Chem.Int.Ed.Engl. 64 e202413651 e202413651 (2025)
PMID: 39363740 DOI: 10.1002/anie.202413651

Abstact

The chemical synthesis of histones with homogeneous modifications is a powerful approach for quantitatively deciphering the functional crosstalk between different post-translational modifications (PTMs). In this study, we developed an expedient site-specific (poly)ubiquitylation strategy (CAEPL, Cysteine Aminoethylation coupled with Enzymatic Protein Ligation), which integrates the Cys-aminoethylation reaction with the process of ubiquitin-activating enzyme UBA1-assisted native chemical ligation. Using this strategy, we successfully prepared monoubiquitylated and K63-linked di- and tri-ubiquitylated linker histone H1.0 proteins, which were incorporated into individual chromatosomes. Quantitative biochemical analysis of different RNF168 constructs on H1 ubiquitylated chromatosomes with different ubiquitin chain lengths demonstrated that K63-linked polyubiquitylated H1.0 could directly stimulate RNF168 ubiquitylation activity by enhancing the affinity between RNF168 and the chromatosome. Subsequent cryo-EM structural analysis of the RNF168/UbcH5c-Ub/H1.0-K63-Ub3 chromatosome complex revealed the potential recruitment orientation between RNF168 UDM1 domain and K63-linked ubiquitin chain on H1.0. Finally, we explored the impact of H1.0 ubiquitylation on RNF168 activity in the context of asymmetric H1.0-K63-Ub3 di-nucleosome substrate, revealing a comparable stimulation effect of both the inter- and intra-nucleosomal crosstalk. Overall, our study highlights the significance of access to structurally defined polyubiquitylated H1.0 by the CAEPL strategy, enabling in-depth mechanistic investigations of in-trans PTM crosstalk between linker histone H1.0 and core histone H2A ubiquitylation.

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