4e8u: Difference between revisions

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==Crystal structure of Arabidopsis IDN2 XS domain along with a small segment of adjacent coiled-coil region==
==Crystal structure of Arabidopsis IDN2 XS domain along with a small segment of adjacent coiled-coil region==
<StructureSection load='4e8u' size='340' side='right' caption='[[4e8u]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='4e8u' size='340' side='right'caption='[[4e8u]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4e8u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8U FirstGlance]. <br>
<table><tr><td colspan='2'>[[4e8u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8U FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.701&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IDN2, T8P19.180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8u OCA], [http://pdbe.org/4e8u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e8u RCSB], [http://www.ebi.ac.uk/pdbsum/4e8u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8u ProSAT]</span></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=4e8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8u OCA], [https://pdbe.org/4e8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8u RCSB], [https://www.ebi.ac.uk/pdbsum/4e8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8u ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/IDN2_ARATH IDN2_ARATH] Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway (PubMed:22570638, PubMed:22592791) and downstream of small interfering RNA (siRNA) formation (PubMed:22810086). Required for de novo DNA methylation, siRNA accumulation and siRNA-mediated maintenance methylation (PubMed:19915591). Required for several post-transcriptional gene silencing pathways (PubMed:20059743). Binds double-stranded RNAs (dsRNAs) with 5'-overhangs through its XS domain (PubMed:19915591, PubMed:20059743). Binds long non-coding RNA (lncRNA) in an AGO4-dependent manner and associates with DRM2, resulting in DNA methylation of RdDM target loci (PubMed:23246435, PubMed:24862207). Mediates the silencing of a subset of MORC6 target loci (PubMed:27171427).<ref>PMID:19915591</ref> <ref>PMID:20059743</ref> <ref>PMID:22570638</ref> <ref>PMID:22592791</ref> <ref>PMID:22810086</ref> <ref>PMID:23246435</ref> <ref>PMID:24862207</ref> <ref>PMID:27171427</ref>  
At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.
 
INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.,Ausin I, Greenberg MV, Simanshu DK, Hale CJ, Vashisht AA, Simon SA, Lee TF, Feng S, Espanola SD, Meyers BC, Wohlschlegel JA, Patel DJ, Jacobsen SE Proc Natl Acad Sci U S A. 2012 May 29;109(22):8374-81. Epub 2012 May 16. PMID:22592791<ref>PMID:22592791</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4e8u" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arath]]
[[Category: Arabidopsis thaliana]]
[[Category: Patel, D J]]
[[Category: Large Structures]]
[[Category: Simanshu, D K]]
[[Category: Patel DJ]]
[[Category: Rna]]
[[Category: Simanshu DK]]
[[Category: Rna binding protein]]
[[Category: Rna directed dna methylation]]
[[Category: Xs domain]]
Retrieved from "https://proteopedia.org/4e8u"