5zwx

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

spinqualitylabelsall models 5zwx, resolution 1.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5zwx is a 4 chain structure with sequence from Arabidopsis thaliana and Raphanus sativus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.9Å Ligands: MLY, MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A0A493R6M0_RAPSA Publication Abstract from PubMed 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. Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin.,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 WA, He XJ, Zhang H, Bressan RA, Du J, Zhu JK Nat Commun. 2018 Oct 31;9(1):4547. doi: 10.1038/s41467-018-06965-w. PMID:30382101 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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