6d3p: Difference between revisions

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<StructureSection load='6d3p' size='340' side='right'caption='[[6d3p]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='6d3p' size='340' side='right'caption='[[6d3p]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6d3p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D3P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6D3P FirstGlance]. <br>
<table><tr><td colspan='2'>[[6d3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sweet_clover_necrotic_mosaic_virus Sweet clover necrotic mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D3P FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</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]] 2.9&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6d3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d3p OCA], [http://pdbe.org/6d3p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d3p RCSB], [http://www.ebi.ac.uk/pdbsum/6d3p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d3p ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</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=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>
</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__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Akiyama, B M]]
[[Category: Sweet clover necrotic mosaic virus]]
[[Category: Costantino, D A]]
[[Category: Akiyama BM]]
[[Category: Kieft, J S]]
[[Category: Costantino DA]]
[[Category: Nix, J C]]
[[Category: Kieft JS]]
[[Category: Sit, T L]]
[[Category: Nix JC]]
[[Category: Steckelberg, A L]]
[[Category: Sit TL]]
[[Category: Exoribonuclease resistance]]
[[Category: Steckelberg A-L]]
[[Category: Rna]]
[[Category: Rna maturation]]
[[Category: Viral non-coding rna]]

Latest revision as of 17:32, 13 March 2024

Crystal structure of an exoribonuclease-resistant RNA from Sweet clover necrotic mosaic virus (SCNMV)Crystal structure of an exoribonuclease-resistant RNA from Sweet clover necrotic mosaic virus (SCNMV)

Structural highlights

6d3p is a 1 chain structure with sequence from Sweet clover necrotic mosaic virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

6d3p, resolution 2.90Å

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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