1ajf - Revision history

OCA at 11:22, 2 August 2023

OCA — Wed, 02 Aug 2023 11:22:18 GMT

←Older revision		Revision as of 11:22, 2 August 2023
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE==		==SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE==
-	<StructureSection load='1ajf' size='340' side='right'caption='[[1ajf~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1ajf' size='340' side='right'caption='[[1ajf]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AJF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [https://pdbe.org/1ajf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [https://www.ebi.ac.uk/pdbsum/1ajf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ajf 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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [https://pdbe.org/1ajf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [https://www.ebi.ac.uk/pdbsum/1ajf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ajf ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Junior, I Tinoco~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Kieft~~, J S~~]]	+	[[Category: Kieft JS]]
-	[[Category: ~~Metal binding]]~~	+	[[Category: Tinoco Junior I]]
-	~~[[Category: Ribonucleic acid]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna structure~~]]	+

OCA at 10:21, 17 February 2021

OCA — Wed, 17 Feb 2021 10:21:20 GMT

←Older revision		Revision as of 10:21, 17 February 2021
Line 3:		Line 3:
	<StructureSection load='1ajf' size='340' side='right'caption='[[1ajf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1ajf' size='340' side='right'caption='[[1ajf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1AJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AJF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [~~http~~://pdbe.org/1ajf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ajf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ajf 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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [https://pdbe.org/1ajf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [https://www.ebi.ac.uk/pdbsum/1ajf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ajf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:34, 10 May 2019

OCA — Fri, 10 May 2019 14:34:33 GMT

←Older revision		Revision as of 14:34, 10 May 2019
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE==		==SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE==
-	<StructureSection load='1ajf' size='340' side='right' caption='[[1ajf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1ajf' size='340' side='right'caption='[[1ajf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Junior, I Tinoco]]		[[Category: Junior, I Tinoco]]
	[[Category: Kieft, J S]]		[[Category: Kieft, J S]]

OCA at 09:25, 9 August 2017

OCA — Wed, 09 Aug 2017 09:25:49 GMT

←Older revision		Revision as of 09:25, 9 August 2017
Line 1:		Line 1:
		+
	==SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE==		==SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE==
	<StructureSection load='1ajf' size='340' side='right' caption='[[1ajf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1ajf' size='340' side='right' caption='[[1ajf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [http://pdbe.org/1ajf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [http://www.ebi.ac.uk/pdbsum/1ajf 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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [http://pdbe.org/1ajf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [http://www.ebi.ac.uk/pdbsum/1ajf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ajf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:00, 11 September 2015

OCA — Fri, 11 Sep 2015 13:00:24 GMT

←Older revision		Revision as of 13:00, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [http://www.ebi.ac.uk/pdbsum/1ajf 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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [http://pdbe.org/1ajf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [http://www.ebi.ac.uk/pdbsum/1ajf PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 1ajf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:46, 22 December 2014

OCA — Mon, 22 Dec 2014 11:46:06 GMT

←Older revision		Revision as of 11:46, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [http://www.ebi.ac.uk/pdbsum/1ajf 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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [http://www.ebi.ac.uk/pdbsum/1ajf 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 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Junior, I Tinoco.]]	+	[[Category: Junior, I Tinoco]]
-	[[Category: Kieft, J S.]]	+	[[Category: Kieft, J S]]
	[[Category: Metal binding]]		[[Category: Metal binding]]
	[[Category: Ribonucleic acid]]		[[Category: Ribonucleic acid]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Rna structure]]		[[Category: Rna structure]]

OCA at 08:16, 30 July 2014

OCA — Wed, 30 Jul 2014 08:16:54 GMT

←Older revision		Revision as of 08:16, 30 July 2014
Line 1:		Line 1:
-	[[~~Image:~~1ajf.~~png~~\|~~left\|200px~~]]	+	==SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE==
		+	<StructureSection load='1ajf' size='340' side='right' caption='[[1ajf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AJF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene><br>
		+	<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=1ajf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ajf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ajf RCSB], [http://www.ebi.ac.uk/pdbsum/1ajf PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Solvated metal ions are critical for the proper folding and function of RNA. Despite the importance of these ions, the details of specific metal ion-RNA interactions are poorly understood. The crystal structure of a group I intron ribozyme domain characterized several metal-binding sites in the RNA with osmium (III) hexammine bound in the major groove. A corresponding method for locating and characterizing metal-binding sites of RNA in solution is of obvious interest. NMR should be ideal for localizing metal hexammine ions bound to the RNA because of the large concentration of protons around the metal center. RESULTS: We have solved the solution structure of the P5b stem loop from a group I intron ribozyme bound to a cobalt (III) hexammine ion. The location of the ion is precisely determined by intermolecular nuclear Overhausser effect cross-peaks between the cobalt (III) hexammine protons and both exchangeable and non-exchangeable RNA protons in the major groove. The binding site consists of tandem G-U base pairs in a sequence of four consecutive G residues ending in a GAAA tetraloop, as originally identified in the crystal structure. The edges of the bases in the major groove present an electrostatically negative face and a variety of hydrogen-bond acceptors for the cobalt (III) hexammine ion. The metal ion ligand is bound near the guanosine nucleotides of the adjacent G-U base pairs, where it makes hydrogen bonds with the N7 and carbonyl groups of both guanines. The carbonyl groups of the uracil residues add to the negative surface of the binding pocket, but do not form hydrogen bonds with the hexammine. Additional hydrogen bonds form with other guanine residues of the GGGG sequence. The structure of the binding site does not change significantly on binding the cobalt (III) hexammine. The structure of the complex in solution is very similar to the structure in the crystal. CONCLUSIONS: The structure presents a picture of how tandem G-U base pairs bind and position metal ions within the RNA major groove. The binding site is performed in the absence of metal ions, and presents a negative pocket in the major groove with a variety of hydrogen-bond acceptors. Because G-U base pairs are such a common motif in RNA sequences, it is possible that this RNA-metal ion interaction is critical in forming large complex RNA structures such as those found in the ribosome and self-splicing introns. This structure was determined using cobalt (III) hexammine as an analog for hexahydrated magnesium, a technique that may be applicable to other RNA sequences. Metal hexammines may prove to be useful general probes for locating RNA metal ion binding sites in solution.

-	~~{{STRUCTURE_1ajf\| PDB=1ajf \| SCENE= }}~~	+	Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine.,Kieft JS, Tinoco I Jr Structure. 1997 May 15;5(5):713-21. PMID:9195889<ref>PMID:9195889</ref>

-	~~===SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE~~, ~~NMR, MINIMIZED AVERAGE STRUCTURE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9195889}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1ajf]] is a 1 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA].~~	+	</StructureSection>
	[[Category: Junior, I Tinoco.]]		[[Category: Junior, I Tinoco.]]
	[[Category: Kieft, J S.]]		[[Category: Kieft, J S.]]

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

OCA — Sun, 21 Oct 2012 12:24:24 GMT

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

←Older revision

Revision as of 12:24, 21 October 2012

OCA at 12:24, 21 October 2012

OCA — Sun, 21 Oct 2012 12:24:21 GMT

←Older revision		Revision as of 12:24, 21 October 2012
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-	{{Seed}}
	[[Image:1ajf.png\|left\|200px]]		[[Image:1ajf.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1ajf\| PDB=1ajf \| SCENE= }}		{{STRUCTURE_1ajf\| PDB=1ajf \| SCENE= }}

	===SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE===		===SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE===

-
-	<!--
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	{{ABSTRACT_PUBMED_9195889}}		{{ABSTRACT_PUBMED_9195889}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA].	+	[[1ajf]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA].
-		+
-	~~==Reference==~~	+
-	Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine., Kieft JS, Tinoco I Jr, Structure. 1997 May 15;5(5):713-21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9195889 9195889]	+
	[[Category: Junior, I Tinoco.]]		[[Category: Junior, I Tinoco.]]
	[[Category: Kieft, J S.]]		[[Category: Kieft, J S.]]
	[[Category: Metal binding]]		[[Category: Metal binding]]
-	[[Category: Nmr]]
	[[Category: Ribonucleic acid]]		[[Category: Ribonucleic acid]]
		+	[[Category: Rna]]
	[[Category: Rna structure]]		[[Category: Rna structure]]
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-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 16:58:44 2008''

OCA at 13:58, 30 June 2008

OCA — Mon, 30 Jun 2008 13:58:46 GMT

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	{{STRUCTURE_1ajf\| PDB=1ajf \| SCENE= }}		{{STRUCTURE_1ajf\| PDB=1ajf \| SCENE= }}

-	~~'''~~SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE~~'''~~	+	===SOLUTION STRUCTURE OF THE P5B STEM LOOP FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE===


-	~~==Overview==~~	+	<!--
-	~~BACKGROUND: Solvated metal ions are critical for the proper folding and function of RNA. Despite the importance of these ions~~, the ~~details of specific metal ion-RNA interactions are poorly understood. The crystal structure of a group I intron ribozyme domain characterized several metal-binding sites in~~ the ~~RNA with osmium~~ (III) hexammine bound in the major groove. A corresponding method for locating and characterizing metal-binding sites of RNA in solution is of obvious interest. NMR should be ideal for localizing metal hexammine ions bound to the RNA because of the large concentration of protons around the metal center. RESULTS: ~~We have solved the solution structure of the P5b stem loop from a group I intron ribozyme bound to a cobalt (III) hexammine ion~~. The location of the ion is precisely determined by intermolecular nuclear Overhausser effect cross-peaks between the cobalt (III) hexammine protons and both exchangeable and non-exchangeable RNA protons in the major groove. The binding site consists of tandem G-U base pairs in a sequence of four consecutive G residues ending in a GAAA tetraloop, as originally identified in the crystal structure. The edges of the bases in the major groove present an electrostatically negative face and a variety of hydrogen-bond acceptors for the cobalt (III) ~~hexammine ion. The metal ion ligand is bound near the guanosine nucleotides of the adjacent G-U base pairs~~, where it makes hydrogen bonds with the N7 and carbonyl groups of both guanines. The carbonyl groups of the uracil residues add to the negative surface of the binding pocket, but do not form hydrogen bonds with the hexammine. Additional hydrogen bonds form with other guanine residues of the GGGG sequence. The structure of the binding site does not change significantly on binding the cobalt (III) hexammine. The structure of the complex in solution is ~~very similar to~~ the ~~structure in the crystal~~. ~~CONCLUSIONS: The structure presents a picture of how tandem G~~-U base pairs bind and position metal ions within the RNA major groove. The binding site is performed in the absence of metal ions, and presents a negative pocket in the major groove with a variety of hydrogen-bond acceptors. Because G-U base pairs are such a common motif in RNA sequences, it is possible that this RNA-metal ion interaction is critical in forming large complex RNA structures such as those found in the ribosome and self-splicing introns. This structure was determined using cobalt (III) hexammine as an analog for hexahydrated magnesium, a technique that may be applicable to other RNA sequences. Metal hexammines may prove to be useful general probes for locating RNA metal ion binding sites in solution.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9195889}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9195889 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9195889}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AJF OCA].

	==Reference==		==Reference==
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	[[Category: Ribonucleic acid]]		[[Category: Ribonucleic acid]]
	[[Category: Rna structure]]		[[Category: Rna structure]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May 2 10~~:21:01 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 16:58:44 2008''