6e1w: Difference between revisions

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<StructureSection load='6e1w' size='340' side='right'caption='[[6e1w]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
<StructureSection load='6e1w' size='340' side='right'caption='[[6e1w]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6e1w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E1W FirstGlance]. <br>
<table><tr><td colspan='2'>[[6e1w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E1W FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HNG:2-amino-5-(aminomethyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one'>HNG</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]] 1.69&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HNG:2-amino-5-(aminomethyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one'>HNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene></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=6e1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e1w OCA], [http://pdbe.org/6e1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e1w RCSB], [http://www.ebi.ac.uk/pdbsum/6e1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e1w ProSAT]</span></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=6e1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e1w OCA], [https://pdbe.org/6e1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e1w RCSB], [https://www.ebi.ac.uk/pdbsum/6e1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e1w ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Riboswitches are naturally occurring RNA aptamers that regulate gene expression by binding to specific small molecules. Riboswitches control the expression of essential bacterial genes and are important models for RNA-small molecule recognition. Here, we report the discovery of a class of synthetic small molecules that bind to PreQ1 riboswitch aptamers. These molecules bind specifically and reversibly to the aptamers with high affinity and induce a conformational change. Furthermore, the ligands modulate riboswitch activity through transcriptional termination despite no obvious chemical similarity to the cognate ligand. X-ray crystallographic studies reveal that the ligands share a binding site with the cognate ligand but make different contacts. Finally, alteration of the chemical structure of the ligand causes changes in the mode of RNA binding and affects regulatory function. Thus, target- and structure-based approaches can be used to identify and understand the mechanism of synthetic ligands that bind to and regulate complex, folded RNAs.


Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.,Connelly CM, Numata T, Boer RE, Moon MH, Sinniah RS, Barchi JJ, Ferre-D'Amare AR, Schneekloth JS Jr Nat Commun. 2019 Apr 2;10(1):1501. doi: 10.1038/s41467-019-09493-3. PMID:30940810<ref>PMID:30940810</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 6e1w" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Amare, A R.Ferre-D]]
[[Category: Connelly CM]]
[[Category: Connelly, C M]]
[[Category: Ferre-D'Amare AR]]
[[Category: Numata, T]]
[[Category: Numata T]]
[[Category: Schneekloth, J S]]
[[Category: Schneekloth JS]]
[[Category: Complex]]
[[Category: Preq1 riboswitch]]
[[Category: Rna]]
[[Category: Synthetic compound]]

Latest revision as of 14:38, 13 March 2024

Crystal structure of a class I PreQ1 riboswitch complexed with PreQ1

6e1w, resolution 1.69Å

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