5ZWX

Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide

Summary for 5ZWX

• Entry DOI: 10.2210/pdb5zwx/pdb
• Descriptor: DUF724 domain-containing protein 6-like, H3(1-15)K9me2 peptide (3 entities in total)
• Functional Keywords: agenet domain, agdp1, epigenetics, h3k9me2, gene regulation
• Biological source: Raphanus sativus; More
• Total number of polymer chains: 4
• Total formula weight: 40452.34

Authors

Du, X.,Du, J. (deposition date: 2018-05-17, release date: 2018-11-14, Last modification date: 2025-04-09)

Primary citation

Zhang, C.,Du, X.,Tang, K.,Yang, Z.,Pan, L.,Zhu, P.,Luo, J.,Jiang, Y.,Zhang, H.,Wan, H.,Wang, X.,Wu, F.,Tao, W.A.,He, X.J.,Zhang, H.,Bressan, R.A.,Du, J.,Zhu, J.K.
Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
Nat Commun, 9:4547-4547, 2018

PubMed Abstract: Heterochromatin is a tightly packed form of chromatin that is associated with DNA methylation and histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2-binding protein, Agenet domain (AGD)-containing p1 (AGDP1), in Arabidopsis thaliana. Here we find that AGDP1 can specifically recognize the H3K9me2 mark by its three pairs of tandem AGDs. We determine the crystal structure of the Agenet domain 1 and 2 cassette (AGD12) of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 specifically recognizes the H3K4me0 and H3K9me2 marks by hydrogen bonding and hydrophobic interactions. In addition, we find that AGDP1 is required for transcriptional silencing, non-CG DNA methylation, and H3K9 dimethylation at some loci. ChIP-seq data show that AGDP1 preferentially occupies long transposons and is associated with heterochromatin marks. Our findings suggest that, as a heterochromatin-binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.

PubMed: 30382101
DOI: 10.1038/s41467-018-06965-w

Experimental method

X-RAY DIFFRACTION (1.9 Å)