3vrs: Difference between revisions

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<StructureSection load='3vrs' size='340' side='right'caption='[[3vrs]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='3vrs' size='340' side='right'caption='[[3vrs]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3vrs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VRS FirstGlance]. <br>
<table><tr><td colspan='2'>[[3vrs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_petrophila Thermotoga petrophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VRS FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.603&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4en5|4en5]], [[4ena|4ena]], [[4enb|4enb]], [[4enc|4enc]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=3vrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrs OCA], [https://pdbe.org/3vrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vrs RCSB], [https://www.ebi.ac.uk/pdbsum/3vrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrs 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=3vrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrs OCA], [https://pdbe.org/3vrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vrs RCSB], [https://www.ebi.ac.uk/pdbsum/3vrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrs ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A*U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg(2+) ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.
Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.,Ren A, Rajashankar KR, Patel DJ Nature. 2012 May 13;486(7401):85-9. doi: 10.1038/nature11152. PMID:22678284<ref>PMID:22678284</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3vrs" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Patel, D J]]
[[Category: Thermotoga petrophila]]
[[Category: Rajashankar, K R]]
[[Category: Patel DJ]]
[[Category: Ren, A M]]
[[Category: Rajashankar KR]]
[[Category: Pseudoknot]]
[[Category: Ren AM]]
[[Category: Rna]]

Latest revision as of 17:28, 14 March 2024

Crystal structure of fluoride riboswitch, soaked in Mn2+Crystal structure of fluoride riboswitch, soaked in Mn2+

Structural highlights

3vrs is a 1 chain structure with sequence from Thermotoga petrophila. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.603Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3vrs, resolution 2.60Å

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