5SZC

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14

Summary for 5SZC

• Entry DOI: 10.2210/pdb5szc/pdb
• Related: 5SZB
• Descriptor: Zinc finger protein DPF3, Histone H3 tail peptide, ZINC ION, ... (5 entities in total)
• Functional Keywords: chromatin, modified histone, phd domain, zinc binding domain, baf45, baf complex, metal binding protein, peptide-binding protein, peptide binding protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 15264.80

Authors

Singh, N.,Local, A.,Shiau, A.,Ren, B.,Corbett, K.D. (deposition date: 2016-08-13, release date: 2017-08-16, Last modification date: 2023-11-15)

Primary citation

Local, A.,Huang, H.,Albuquerque, C.P.,Singh, N.,Lee, A.Y.,Wang, W.,Wang, C.,Hsia, J.E.,Shiau, A.K.,Ge, K.,Corbett, K.D.,Wang, D.,Zhou, H.,Ren, B.
Identification of H3K4me1-associated proteins at mammalian enhancers.
Nat. Genet., 50:73-82, 2018

PubMed Abstract: Enhancers act to regulate cell-type-specific gene expression by facilitating the transcription of target genes. In mammalian cells, active or primed enhancers are commonly marked by monomethylation of histone H3 at lysine 4 (H3K4me1) in a cell-type-specific manner. Whether and how this histone modification regulates enhancer-dependent transcription programs in mammals is unclear. In this study, we conducted SILAC mass spectrometry experiments with mononucleosomes and identified multiple H3K4me1-associated proteins, including many involved in chromatin remodeling. We demonstrate that H3K4me1 augments association of the chromatin-remodeling complex BAF to enhancers in vivo and that, in vitro, H3K4me1-marked nucleosomes are more efficiently remodeled by the BAF complex. Crystal structures of the BAF component BAF45C indicate that monomethylation, but not trimethylation, is accommodated by BAF45C's H3K4-binding site. Our results suggest that H3K4me1 has an active role at enhancers by facilitating binding of the BAF complex and possibly other chromatin regulators.

PubMed: 29255264
DOI: 10.1038/s41588-017-0015-6

Experimental method

X-RAY DIFFRACTION (1.193 Å)