3d0x: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3d0x.png|left|200px]]
-<!--
+==Crystal Structure of the unbound lysine riboswitch==
-The line below this paragraph, containing "STRUCTURE_3d0x", creates the "Structure Box" on the page.
+<StructureSection load='3d0x' size='340' side='right'caption='[[3d0x]], [[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'>[[3d0x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D0X 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d0x OCA], [https://pdbe.org/3d0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d0x RCSB], [https://www.ebi.ac.uk/pdbsum/3d0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d0x ProSAT]</span></td></tr>
-{{STRUCTURE_3d0x|  PDB=3d0x  |  SCENE=  }}
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Riboswitches are metabolite-sensitive elements found in mRNAs that control gene expression through a regulatory secondary structural switch. Along with regulation of lysine biosynthetic genes, mutations within the lysine-responsive riboswitch (L-box) play a role in the acquisition of resistance to antimicrobial lysine analogs. To understand the structural basis for lysine binding, we have determined the 2.8 angstroms resolution crystal structure of lysine bound to the Thermotoga maritima asd lysine riboswitch ligand-binding domain. The structure reveals a complex architecture scaffolding a binding pocket completely enveloping lysine. Mutations conferring antimicrobial resistance cluster around this site as well as highly conserved long range interactions, indicating that they disrupt lysine binding or proper folding of the RNA. Comparison of the free and bound forms by x-ray crystallography, small angle x-ray scattering, and chemical probing reveals almost identical structures, indicating that lysine induces only limited and local conformational changes upon binding.
-===Crystal Structure of the unbound lysine riboswitch===
+Crystal structure of the lysine riboswitch regulatory mRNA element.,Garst AD, Heroux A, Rambo RP, Batey RT J Biol Chem. 2008 Aug 15;283(33):22347-51. Epub 2008 Jul 1. PMID:18593706<ref>PMID:18593706</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3d0x" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18593706}}, adds the Publication Abstract to the page
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18593706 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18593706}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D0X is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D0X OCA].
+[[Category: Thermotoga maritima]]
+[[Category: Batey RT]]
-==Reference==
+[[Category: Garst AD]]
-Crystal structure of the lysine riboswitch regulatory mRNA element., Garst AD, Heroux A, Rambo RP, Batey RT, J Biol Chem. 2008 Aug 15;283(33):22347-51. Epub 2008 Jul 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18593706 18593706]
+[[Category: Heroux A]]
-[[Category: Single protein]]
+[[Category: Rambo RP]]
-[[Category: Batey, R T.]]
-[[Category: Garst, A D.]]
-[[Category: Heroux, A.]]
-[[Category: Rambo, R P.]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 12:25:38 2008''