3iqr: Difference between revisions

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-{{Seed}}
-[[Image:3iqr.jpg|left|200px]]
-<!--
+==SAM-I riboswitch from T. tencongensis variant A94G bound with SAM==
-The line below this paragraph, containing "STRUCTURE_3iqr", creates the "Structure Box" on the page.
+<StructureSection load='3iqr' size='340' side='right'caption='[[3iqr]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3iqr]] 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=3IQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IQR FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-{{STRUCTURE_3iqr|  PDB=3iqr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3iqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqr OCA], [https://pdbe.org/3iqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iqr RCSB], [https://www.ebi.ac.uk/pdbsum/3iqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iqr ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Riboswitches are highly structured elements residing in the 5' untranslated region of messenger RNAs that specifically bind cellular metabolites to alter gene expression. While there are many structures of ligand-bound riboswitches that reveal details of bimolecular recognition, their unliganded structures remain poorly characterized. Characterizing the molecular details of the unliganded state is crucial for understanding the riboswitch's mechanism of action because it is this state that actively interrogates the cellular environment and helps direct the regulatory outcome. To develop a detailed description of the ligand-free form of an S-adenosylmethionine binding riboswitch at the local and global levels, we have employed a series of biochemical, biophysical, and computational methods. Our data reveal that the ligand binding domain adopts an ensemble of states that minimizes the energy barrier between the free and bound states to establish an efficient decision making branchpoint in the regulatory process.
-===SAM-I riboswitch from T. tencongensis variant A94G bound with SAM===
+Free state conformational sampling of the SAM-I riboswitch aptamer domain.,Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT Structure. 2010 Jul 14;18(7):787-97. PMID:20637415<ref>PMID:20637415</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3iqr" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20637415}}, adds the Publication Abstract to the page
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20637415 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20637415}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
-IQR is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IQR OCA].
+[[Category: Large Structures]]
+[[Category: Batey RT]]
-==Reference==
+[[Category: Montange RK]]
-<ref group="xtra">PMID:20637415</ref><references group="xtra"/>
-[[Category: Batey, R T.]]
-[[Category: Montange, R K.]]
-[[Category: Kink-turn]]
-[[Category: Psuedoknot]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-[[Category: Sam]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug  4 09:07:04 2010''