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| - | [[Image:1f1t.gif|left|200px]] | |
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| - | <!--
| + | ==CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE== |
| - | The line below this paragraph, containing "STRUCTURE_1f1t", creates the "Structure Box" on the page.
| + | <StructureSection load='1f1t' size='340' side='right'caption='[[1f1t]], [[Resolution|resolution]] 2.80Å' 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'>[[1f1t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F1T 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]] 2.8Å</td></tr> |
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| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr> |
| - | {{STRUCTURE_1f1t| PDB=1f1t | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [https://pdbe.org/1f1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [https://www.ebi.ac.uk/pdbsum/1f1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f1t ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Baugh C]] |
| - | Previous in vitro selection experiments identified an RNA aptamer that recognizes the chromophore malachite green (MG) with a high level of affinity, and which undergoes site-specific cleavage following laser irradiation. To understand the mechanism by which this RNA folds to recognize specifically its ligand and the structural basis for chromophore-assisted laser inactivation, we have determined the 2.8 A crystal structure of the aptamer bound to tetramethylrosamine (TMR), a high-affinity MG analog. The ligand-binding site is defined by an asymmetric internal loop, flanked by a pair of helices. A U-turn and several non-canonical base interactions stabilize the folding of loop nucleotides around the TMR. The aptamer utilizes several tiers of stacked nucleotides arranged in pairs, triples, and a novel base quadruple to effectively encapsulate the ligand. Even in the absence of specific stabilizing hydrogen bonds, discrimination between related fluorophores and chromophores is possible due to tight packing in the RNA binding pocket, which severely limits the size and shape of recognized ligands. The site of laser-induced cleavage lies relatively far from the bound TMR ( approximately 15 A). The unusual backbone conformation of the cleavage site nucleotide and its high level of solvent accessibility may combine to allow preferential reaction with freely diffusing hydroxyl radicals generated at the bound ligand. Several observations, however, favor alternative mechanisms for cleavage, such as conformational changes in the aptamer or long-range electron transfer between the bound ligand and the cleavage site nucleotide.
| + | [[Category: Grate D]] |
| - | | + | [[Category: Wilson C]] |
| - | ==About this Structure== | + | |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1T OCA]. | + | |
| - | | + | |
| - | ==Reference== | + | |
| - | 2.8 A crystal structure of the malachite green aptamer., Baugh C, Grate D, Wilson C, J Mol Biol. 2000 Aug 4;301(1):117-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10926496 10926496] | + | |
| - | [[Category: Baugh, C.]] | + | |
| - | [[Category: Grate, D.]] | + | |
| - | [[Category: Wilson, C.]]
| + | |
| - | [[Category: 5-bromo-uridine]] | + | |
| - | [[Category: Base quadruple]] | + | |
| - | [[Category: Base triple]] | + | |
| - | [[Category: Gnra tetraloop]] | + | |
| - | [[Category: U-turn]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:47:07 2008''
| + | |
