5kh8: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 5kh8 is ~~ON HOLD~~

==Solution structures of the apo state fluoride riboswitch==

== Structural highlights ==

<table><tr><td colspan='2'>[[5kh8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KH8 FirstGlance]. <br>

</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=5kh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kh8 OCA], [https://pdbe.org/5kh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kh8 RCSB], [https://www.ebi.ac.uk/pdbsum/5kh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kh8 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Riboswitches control gene expression through ligand-dependent structural rearrangements of the sensing aptamer domain. However, we found that the Bacillus cereus fluoride riboswitch aptamer adopts identical tertiary structures in solution with and without ligand. Using chemical-exchange saturation transfer (CEST) NMR spectroscopy, we revealed that the structured ligand-free aptamer transiently accesses a low-populated ( approximately 1%) and short-lived ( approximately 3 ms) excited conformational state that unravels a conserved 'linchpin' base pair to signal transcription termination. Upon fluoride binding, this highly localized, fleeting process is allosterically suppressed, which activates transcription. We demonstrated that this mechanism confers effective fluoride-dependent gene activation over a wide range of transcription rates, which is essential for robust toxicity responses across diverse cellular conditions. These results unveil a novel switching mechanism that employs ligand-dependent suppression of an aptamer excited state to coordinate regulatory conformational transitions rather than adopting distinct aptamer ground-state tertiary architectures, exemplifying a new mode of ligand-dependent RNA regulation.

~~Authors~~:

An excited state underlies gene regulation of a transcriptional riboswitch.,Zhao B, Guffy SL, Williams B, Zhang Q Nat Chem Biol. 2017 Jul 17. doi: 10.1038/nchembio.2427. PMID:28719589<ref>PMID:28719589</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

==See Also==

*[[Riboswitch 3D structures|Riboswitch 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Synthetic construct]]

[[Category: Zhang Q]]

[[Category: Zhao B]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5kh8 is ON HOLD
+==Solution structures of the apo state fluoride riboswitch==
+<StructureSection load='5kh8' size='340' side='right'caption='[[5kh8]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5kh8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KH8 FirstGlance]. <br>
+</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=5kh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kh8 OCA], [https://pdbe.org/5kh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kh8 RCSB], [https://www.ebi.ac.uk/pdbsum/5kh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kh8 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Riboswitches control gene expression through ligand-dependent structural rearrangements of the sensing aptamer domain. However, we found that the Bacillus cereus fluoride riboswitch aptamer adopts identical tertiary structures in solution with and without ligand. Using chemical-exchange saturation transfer (CEST) NMR spectroscopy, we revealed that the structured ligand-free aptamer transiently accesses a low-populated ( approximately 1%) and short-lived ( approximately 3 ms) excited conformational state that unravels a conserved 'linchpin' base pair to signal transcription termination. Upon fluoride binding, this highly localized, fleeting process is allosterically suppressed, which activates transcription. We demonstrated that this mechanism confers effective fluoride-dependent gene activation over a wide range of transcription rates, which is essential for robust toxicity responses across diverse cellular conditions. These results unveil a novel switching mechanism that employs ligand-dependent suppression of an aptamer excited state to coordinate regulatory conformational transitions rather than adopting distinct aptamer ground-state tertiary architectures, exemplifying a new mode of ligand-dependent RNA regulation.
-Authors:
+An excited state underlies gene regulation of a transcriptional riboswitch.,Zhao B, Guffy SL, Williams B, Zhang Q Nat Chem Biol. 2017 Jul 17. doi: 10.1038/nchembio.2427. PMID:28719589<ref>PMID:28719589</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5kh8" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Zhang Q]]
+[[Category: Zhao B]]