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==Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3==
==Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3==
<StructureSection load='6bfb' size='340' side='right' caption='[[6bfb]], [[Resolution|resolution]] 2.82&Aring;' scene=''>
<StructureSection load='6bfb' size='340' side='right'caption='[[6bfb]], [[Resolution|resolution]] 2.82&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6bfb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BFB FirstGlance]. <br>
<table><tr><td colspan='2'>[[6bfb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum Fusobacterium nucleatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BFB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DKM:5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic+acid'>DKM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.82&#8491;</td></tr>
<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=6bfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfb OCA], [http://pdbe.org/6bfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bfb RCSB], [http://www.ebi.ac.uk/pdbsum/6bfb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfb ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DKM:5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic+acid'>DKM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6bfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfb OCA], [https://pdbe.org/6bfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bfb RCSB], [https://www.ebi.ac.uk/pdbsum/6bfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfb ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. Here, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule-ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.


Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry.,Rizvi NF, Howe JA, Nahvi A, Klein DJ, Fischmann TO, Kim HY, McCoy MA, Walker SS, Hruza A, Richards MP, Chamberlin C, Saradjian P, Butko MT, Mercado G, Burchard J, Strickland C, Dandliker PJ, Smith GF, Nickbarg EB ACS Chem Biol. 2018 Feb 14. doi: 10.1021/acschembio.7b01013. PMID:29412640<ref>PMID:29412640</ref>
==See Also==
 
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6bfb" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Fischmann, T O]]
[[Category: Fusobacterium nucleatum]]
[[Category: Rizvi, N F]]
[[Category: Large Structures]]
[[Category: Rna]]
[[Category: Fischmann TO]]
[[Category: Rna-inhibitor complex]]
[[Category: Rizvi NF]]
[[Category: Translation]]

Latest revision as of 17:32, 6 March 2024

Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3

Structural highlights

6bfb is a 2 chain structure with sequence from Fusobacterium nucleatum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.82Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

6bfb, resolution 2.82Å

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