3gx7: Difference between revisions

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-{{Seed}}
-[[Image:3gx7.png|left|200px]]
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+==Crystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G mutant A6C/U7G/A87C/U88G bound with SAM==
-The line below this paragraph, containing "STRUCTURE_3gx7", creates the "Structure Box" on the page.
+<StructureSection load='3gx7' size='340' side='right'caption='[[3gx7]], [[Resolution|resolution]] 2.95&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'>[[3gx7]] 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=3GX7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GX7 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]] 2.95&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-{{STRUCTURE_3gx7|  PDB=3gx7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gx7 OCA], [https://pdbe.org/3gx7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gx7 RCSB], [https://www.ebi.ac.uk/pdbsum/3gx7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gx7 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-A X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-A improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.
-===Crystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G mutant A6C/U7G/A87C/U88G bound with SAM===
+Discrimination between closely related cellular metabolites by the SAM-I riboswitch.,Montange RK, Mondragon E, van Tyne D, Garst AD, Ceres P, Batey RT J Mol Biol. 2010 Feb 26;396(3):761-72. Epub 2009 Dec 16. PMID:20006621<ref>PMID:20006621</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20006621}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3gx7" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20006621 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20006621}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
-GX7 is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GX7 OCA].
+[[Category: Large Structures]]
+[[Category: Batey RT]]
-==Reference==
+[[Category: Montange RK]]
-<ref group="xtra">PMID:20006621</ref><references group="xtra"/>
-[[Category: Batey, R T.]]
-[[Category: Montange, R K.]]
-[[Category: Four-way junction]]
-[[Category: Kink-turn]]
-[[Category: Pseudoknot]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar  3 13:19:13 2010''