View source for 9k11


==A cryo-EM structure of B. oleracea RNA polymerase V in complex with 0U scaffold at 2.96 Angstrom==
<StructureSection load='9k11' size='340' side='right'caption='[[9k11]], [[Resolution|resolution]] 2.96&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9k11]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Brassica_oleracea Brassica oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9K11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9K11 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.96&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=9k11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9k11 OCA], [https://pdbe.org/9k11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9k11 RCSB], [https://www.ebi.ac.uk/pdbsum/9k11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9k11 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding RNA guides DNA methylation through the RNA-directed DNA methylation (RdDM) pathway; however, how these RNAs are selected is unknown. Here, we show that the 3'-ends of Pol V transcripts are enriched at A-rich template DNA (A-rich-DNA(T)). Arabidopsis RdDM regions possess AT-rich boundaries genome-wide, suggesting that Pol V likely terminates at A-rich-DNA(T), which subsequently defines the DNA methylation landscape in plants. A-rich-DNA(T) successfully stops Pol V transcription in vitro. Structural snapshots of Pol V transcribing A-rich-DNA(T) show that accumulation of unstable rU:dA pairs in the RNA-DNA hybrid promotes transcription bubble collapse and spontaneous transcription termination. These findings identify an intrinsic Pol V termination signal that shapes genomic DNA methylation patterning in plants and reveals a common mechanism for spontaneous transcription termination.

A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.,Xie G, Du X, Tan Y, Zhou Y, Chi C, Zhou S, Picard CL, Chai S, Wu L, Zhu D, Zhao J, Xue Y, Li S, Jacobsen SE, Wu Z, Du J EMBO J. 2026 Apr 2. doi: 10.1038/s44318-026-00763-7. PMID:41928006<ref>PMID:41928006</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9k11" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Brassica oleracea]]
[[Category: Large Structures]]
[[Category: Du J]]
[[Category: Du X]]
[[Category: Xie G]]