3oxm: Difference between revisions

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-[[Image:3oxm.jpg|left|200px]]
-<!--
+==crystal structure of glycine riboswitch, Tl-Acetate soaked==
-The line below this paragraph, containing "STRUCTURE_3oxm", creates the "Structure Box" on the page.
+<StructureSection load='3oxm' size='340' side='right'caption='[[3oxm]], [[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'>[[3oxm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OXM 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=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>
-{{STRUCTURE_3oxm|  PDB=3oxm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3oxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oxm OCA], [https://pdbe.org/3oxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oxm RCSB], [https://www.ebi.ac.uk/pdbsum/3oxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oxm ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glycine riboswitches regulate gene expression by feedback modulation in response to cooperative binding to glycine. Here, we report on crystal structures of the second glycine-sensing domain from the Vibrio cholerae riboswitch in the ligand-bound and unbound states. This domain adopts a three-helical fold that centers on a three-way junction and accommodates glycine within a bulge-containing binding pocket above the junction. Glycine recognition is facilitated by a pair of bound Mg(2+) cations and governed by specific interactions and shape complementarity with the pocket. A conserved adenine extrudes from the binding pocket and intercalates into the junction implying that glycine binding in the context of the complete riboswitch could impact on gene expression by stabilizing the riboswitch junction and regulatory P1 helix. Analysis of riboswitch interactions in the crystal and footprinting experiments indicates that adjacent glycine-sensing modules of the riboswitch could form specific interdomain interactions, thereby potentially contributing to the cooperative response.
-===crystal structure of glycine riboswitch, Tl-Acetate soaked===
+Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch.,Huang L, Serganov A, Patel DJ Mol Cell. 2010 Dec 10;40(5):774-86. PMID:21145485<ref>PMID:21145485</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3oxm" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21145485}}, adds the Publication Abstract to the page
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21145485 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21145485}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3oxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OXM OCA].
+[[Category: Vibrio cholerae]]
+[[Category: Huang L]]
-==Reference==
+[[Category: Patel DJ]]
-<ref group="xtra">PMID:21145485</ref><references group="xtra"/>
+[[Category: Serganov A]]
-[[Category: Huang, L.]]
-[[Category: Patel, D J.]]
-[[Category: Serganov, A.]]
-[[Category: Gene expression regulator]]
-[[Category: Glycine riboswitch]]
-[[Category: Rna]]