6d3p: Difference between revisions

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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=6d3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d3p OCA], [https://pdbe.org/6d3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d3p RCSB], [https://www.ebi.ac.uk/pdbsum/6d3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d3p ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Folded RNA elements that block processive 5' --> 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These xrRNAs have no sequence similarity to known xrRNAs; thus, we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.

A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.,Steckelberg AL, Akiyama BM, Costantino DA, Sit TL, Nix JC, Kieft JS Proc Natl Acad Sci U S A. 2018 Jun 4. pii: 1802429115. doi:, 10.1073/pnas.1802429115. PMID:29866852<ref>PMID:29866852</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

__TOC__

</StructureSection>

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@@ Line 8: / Line 8: @@
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6d3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d3p OCA], [https://pdbe.org/6d3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d3p RCSB], [https://www.ebi.ac.uk/pdbsum/6d3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d3p ProSAT]</span></td></tr>
 </table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Folded RNA elements that block processive 5' --&gt; 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These xrRNAs have no sequence similarity to known xrRNAs; thus, we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.
+A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.,Steckelberg AL, Akiyama BM, Costantino DA, Sit TL, Nix JC, Kieft JS Proc Natl Acad Sci U S A. 2018 Jun 4. pii: 1802429115. doi:, 10.1073/pnas.1802429115. PMID:29866852<ref>PMID:29866852</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6d3p" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>