View source for 5zwx


==Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide==
<StructureSection load='5zwx' size='340' side='right'caption='[[5zwx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5zwx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Raphanus_sativus Raphanus sativus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZWX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zwx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwx OCA], [https://pdbe.org/5zwx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zwx RCSB], [https://www.ebi.ac.uk/pdbsum/5zwx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A493R6M0_RAPSA A0A493R6M0_RAPSA] 
<div style="background-color:#fffaf0;">
== 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<ref>PMID:30382101</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5zwx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Raphanus sativus]]
[[Category: Du J]]
[[Category: Du X]]