1f1t - Revision history

OCA at 07:09, 7 February 2024

OCA — Wed, 07 Feb 2024 07:09:41 GMT

←Older revision		Revision as of 07:09, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<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>		<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>
-	</td></tr><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>	+	</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>
		+	<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>
	<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>		<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>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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:10926496<ref>PMID:10926496</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1f1t" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:25, 21 December 2022

OCA — Wed, 21 Dec 2022 10:25:31 GMT

←Older revision		Revision as of 10:25, 21 December 2022
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<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>		<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>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=~~ROS~~:~~N,N~~-~~TETRAMETHYL~~-~~ROSAMINE~~'>~~ROS~~</scene>, <scene name='pdbligand=SR:~~STRONTIUM+ION~~'>SR</scene>~~</td></tr>~~	+	</td></tr><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>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~5BU~~:~~5-BROMO-URIDINE-5-MONOPHOSPHATE~~'>~~5BU~~</scene></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=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>		<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>		</table>
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baugh, C]]	+	[[Category: Baugh C]]
-	[[Category: Grate, D]]	+	[[Category: Grate D]]
-	[[Category: Wilson, C]]	+	[[Category: Wilson C]]
-	~~[[Category: 5-bromo-uridine]]~~	+
-	~~[[Category: Base quadruple]]~~	+
-	~~[[Category: Base triple]]~~	+
-	~~[[Category: Gnra tetraloop]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: U-turn~~]]	+

OCA at 07:18, 17 March 2021

OCA — Wed, 17 Mar 2021 07:18:05 GMT

←Older revision		Revision as of 07:18, 17 March 2021
Line 3:		Line 3:
	<StructureSection load='1f1t' size='340' side='right'caption='[[1f1t]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1f1t' size='340' side='right'caption='[[1f1t]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F1T FirstGlance]. <br>	+	<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>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [~~http~~://pdbe.org/1f1t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f1t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f1t ProSAT]</span></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=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>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:52, 12 June 2019

OCA — Wed, 12 Jun 2019 06:52:34 GMT

←Older revision		Revision as of 06:52, 12 June 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE==		==CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE==
-	<StructureSection load='1f1t' size='340' side='right' caption='[[1f1t]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1f1t' size='340' side='right'caption='[[1f1t]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F1T FirstGlance]. <br>		<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F1T FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baugh, C]]		[[Category: Baugh, C]]
	[[Category: Grate, D]]		[[Category: Grate, D]]

OCA at 04:01, 6 September 2017

OCA — Wed, 06 Sep 2017 04:01:01 GMT

←Older revision		Revision as of 04:01, 6 September 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE==		==CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE==
	<StructureSection load='1f1t' size='340' side='right' caption='[[1f1t]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1f1t' size='340' side='right' caption='[[1f1t]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [http://pdbe.org/1f1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [http://www.ebi.ac.uk/pdbsum/1f1t PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [http://pdbe.org/1f1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [http://www.ebi.ac.uk/pdbsum/1f1t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f1t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:52, 9 September 2015

OCA — Wed, 09 Sep 2015 20:52:01 GMT

←Older revision		Revision as of 20:52, 9 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [http://www.ebi.ac.uk/pdbsum/1f1t PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [http://pdbe.org/1f1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [http://www.ebi.ac.uk/pdbsum/1f1t PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1f1t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:22, 22 December 2014

OCA — Mon, 22 Dec 2014 05:22:31 GMT

←Older revision		Revision as of 05:22, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F1T FirstGlance]. <br>		<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F1T FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [http://www.ebi.ac.uk/pdbsum/1f1t PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [http://www.ebi.ac.uk/pdbsum/1f1t PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baugh, C.]]	+	[[Category: Baugh, C]]
-	[[Category: Grate, D.]]	+	[[Category: Grate, D]]
-	[[Category: Wilson, C.]]	+	[[Category: Wilson, C]]
	[[Category: 5-bromo-uridine]]		[[Category: 5-bromo-uridine]]
	[[Category: Base quadruple]]		[[Category: Base quadruple]]

OCA at 05:53, 8 June 2014

OCA — Sun, 08 Jun 2014 05:53:48 GMT

←Older revision		Revision as of 05:53, 8 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1f1t.~~png~~\|~~left~~\|~~200px~~]]	+	==CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE==
		+	<StructureSection load='1f1t' size='340' side='right' caption='[[1f1t]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F1T FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ROS:N,N-TETRAMETHYL-ROSAMINE'>ROS</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f1t RCSB], [http://www.ebi.ac.uk/pdbsum/1f1t PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_1f1t\| PDB=1f1t \| SCENE= }}~~	+	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:10926496<ref>PMID:10926496</ref>

-	~~===CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10926496}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1f1t]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1F1T OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010926496<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Baugh, C.]]		[[Category: Baugh, C.]]
	[[Category: Grate, D.]]		[[Category: Grate, D.]]

OCA: Protected "1f1t" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 15:33:15 GMT

Protected "1f1t" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:33, 14 August 2012

OCA at 15:33, 14 August 2012

OCA — Tue, 14 Aug 2012 15:33:13 GMT

←Older revision		Revision as of 15:33, 14 August 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1f1t.png\|left\|200px]]		[[Image:1f1t.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1f1t", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1f1t\| PDB=1f1t \| SCENE= }}		{{STRUCTURE_1f1t\| PDB=1f1t \| SCENE= }}

	===CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE===		===CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10926496}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10926496 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10926496}}		{{ABSTRACT_PUBMED_10926496}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1T OCA].	+	[[1f1t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1T OCA].

	==Reference==		==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]~~	+	<ref group="xtra">PMID:010926496</ref><references group="xtra"/>
	[[Category: Baugh, C.]]		[[Category: Baugh, C.]]
	[[Category: Grate, D.]]		[[Category: Grate, D.]]
Line 31:		Line 19:
	[[Category: Base triple]]		[[Category: Base triple]]
	[[Category: Gnra tetraloop]]		[[Category: Gnra tetraloop]]
		+	[[Category: Rna]]
	[[Category: U-turn]]		[[Category: U-turn]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 02:20:50 2008''