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5z9x

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Current revision (10:27, 27 March 2024) (edit) (undo)
 
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==Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate==
==Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate==
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<StructureSection load='5z9x' size='340' side='right' caption='[[5z9x]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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<StructureSection load='5z9x' size='340' side='right'caption='[[5z9x]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5z9x]] 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=5Z9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z9X FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5z9x]] 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=5Z9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z9X FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SDN1, At3g50100, F3A4.180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
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<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=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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=5z9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z9x OCA], [http://pdbe.org/5z9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z9x RCSB], [http://www.ebi.ac.uk/pdbsum/5z9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z9x ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5z9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z9x OCA], [https://pdbe.org/5z9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z9x RCSB], [https://www.ebi.ac.uk/pdbsum/5z9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z9x ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/SDN1_ARATH SDN1_ARATH]] 3'-5' exonuclease degrading single-stranded small RNAs.<ref>PMID:18787168</ref>
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[https://www.uniprot.org/uniprot/SDN1_ARATH SDN1_ARATH] 3'-5' exonuclease degrading single-stranded small RNAs.<ref>PMID:18787168</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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A family of DEDDh 3'--&gt;5' exonucleases known as Small RNA Degrading Nucleases (SDNs) initiates the turnover of ARGONAUTE1 (AGO1)-bound microRNAs in Arabidopsis by trimming their 3' ends. Here, we report the crystal structure of Arabidopsis SDN1 (residues 2-300) in complex with a 9 nucleotide single-stranded RNA substrate, revealing that the DEDDh domain forms rigid interactions with the N-terminal domain and binds 4 nucleotides from the 3' end of the RNA via its catalytic pocket. Structural and biochemical results suggest that the SDN1 C-terminal domain adopts an RNA Recognition Motif (RRM) fold and is critical for substrate binding and enzymatic processivity of SDN1. In addition, SDN1 interacts with the AGO1 PAZ domain in an RNA-independent manner in vitro, enabling it to act on AGO1-bound microRNAs. These extensive structural and biochemical studies may shed light on a common 3' end trimming mechanism for 3'--&gt;5' exonucleases in the metabolism of small non-coding RNAs.
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Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.,Chen J, Liu L, You C, Gu J, Ruan W, Zhang L, Gan J, Cao C, Huang Y, Chen X, Ma J Nat Commun. 2018 Sep 4;9(1):3585. doi: 10.1038/s41467-018-05942-7. PMID:30181559<ref>PMID:30181559</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5z9x" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Arath]]
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[[Category: Arabidopsis thaliana]]
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[[Category: Cao, C]]
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[[Category: Large Structures]]
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[[Category: Chen, J]]
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[[Category: Cao C]]
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[[Category: Chen, X]]
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[[Category: Chen J]]
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[[Category: Gan, J]]
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[[Category: Chen X]]
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[[Category: Gu, J]]
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[[Category: Gan J]]
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[[Category: Huang, Y]]
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[[Category: Gu J]]
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[[Category: Liu, L]]
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[[Category: Huang Y]]
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[[Category: Ma, J]]
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[[Category: Liu L]]
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[[Category: Ruan, W]]
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[[Category: Ma J]]
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[[Category: You, C]]
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[[Category: Ruan W]]
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[[Category: Zhang, L]]
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[[Category: You C]]
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[[Category: Exonuclease]]
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[[Category: Zhang L]]
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[[Category: Microrna turnover]]
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[[Category: Plant protein]]
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[[Category: Plant protein-rna complex]]
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[[Category: Protein-rna complex]]
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Current revision

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate

PDB ID 5z9x

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