7a9w: Difference between revisions

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-'''Unreleased structure'''
-The entry 7a9w is ON HOLD  until Paper Publication
+==Structure of yeast Rmd9p in complex with 20nt target RNA==
+<StructureSection load='7a9w' size='340' side='right'caption='[[7a9w]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7a9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7A9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7A9W 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]] 2.55&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAS:S-(DIMETHYLARSENIC)CYSTEINE'>CAS</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=7a9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7a9w OCA], [https://pdbe.org/7a9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7a9w RCSB], [https://www.ebi.ac.uk/pdbsum/7a9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7a9w ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RMD9_YEAST RMD9_YEAST] Binds the RNA motif 5'-AAUAA[U/C]AUUCUU-3' in the 3'-UTR of mitochondrial mRNAs (PubMed:10441495, PubMed:10905425, PubMed:33876744). Involved in the processing or stability of mitochondrial mRNAs (PubMed:17194786, PubMed:17194787, PubMed:33876744).<ref>PMID:10441495</ref> <ref>PMID:10905425</ref> <ref>PMID:17194786</ref> <ref>PMID:17194787</ref> <ref>PMID:33876744</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5' capping and 3' polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3'-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3'-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.
-Authors: Hillen, H.S., Markov, D.A., Ireneusz, W.D., Hofmann, K.B., Cowan, A.T., Jones, J.L., Temiakov, D., Cramer, P., Anikin, M.
+The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs.,Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2009329118. doi: , 10.1073/pnas.2009329118. PMID:33876744<ref>PMID:33876744</ref>
-Description: Structure of yeast Rmd9p in complex with 20nt target RNA
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Anikin, M]]
+<div class="pdbe-citations 7a9w" style="background-color:#fffaf0;"></div>
-[[Category: Temiakov, D]]
+== References ==
-[[Category: Cowan, A.T]]
+<references/>
-[[Category: Hillen, H.S]]
+__TOC__
-[[Category: Hofmann, K.B]]
+</StructureSection>
-[[Category: Ireneusz, W.D]]
+[[Category: Large Structures]]
-[[Category: Markov, D.A]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Cramer, P]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Jones, J.L]]
+[[Category: Anikin M]]
+[[Category: Cowan AT]]
+[[Category: Cramer P]]
+[[Category: Hillen HS]]
+[[Category: Hofmann KB]]
+[[Category: Ireneusz WD]]
+[[Category: Jones JL]]
+[[Category: Markov DA]]
+[[Category: Temiakov D]]