4rzd: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[4rzd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Faecalibacterium_prausnitzii Faecalibacterium prausnitzii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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]] 2.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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=4rzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzd OCA], [https://pdbe.org/4rzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzd RCSB], [https://www.ebi.ac.uk/pdbsum/4rzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzd ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-PreQ1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, we determined the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 A resolution. PreQ1 binds tightly (KD,app 6.5 +/- 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3' RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ1 enhances P4 reorientation toward P1-P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdock approximately 0.6 s-1) and undocking (kundock approximately 1.1 s-1). Discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.
-Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.,Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE Proc Natl Acad Sci U S A. 2015 Jun 23. pii: 201503955. PMID:26106162<ref>PMID:26106162</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4rzd" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>