3skt - Revision history

OCA at 09:51, 1 March 2024

OCA — Fri, 01 Mar 2024 09:51:30 GMT

←Older revision		Revision as of 09:51, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3skt' size='340' side='right'caption='[[3skt]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3skt' size='340' side='right'caption='[[3skt]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SKT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3skt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesoplasma_florum Mesoplasma florum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SKT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GNG:2~~-~~DEOXY-GUANOSINE'>GNG</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene><~~/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=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max-height: 3em;~~'>~~[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]~~</~~div~~></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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [https://pdbe.org/3skt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [https://www.ebi.ac.uk/pdbsum/3skt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3skt 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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [https://pdbe.org/3skt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [https://www.ebi.ac.uk/pdbsum/3skt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3skt ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Purine riboswitches have an essential role in genetic regulation of bacterial metabolism. This family includes the 2'-deoxyguanosine (dG) riboswitch, which is involved in feedback control of deoxyguanosine biosynthesis. To understand the principles that define dG selectivity, we determined crystal structures of the natural Mesoplasma florum riboswitch bound to cognate dG as well as to noncognate guanosine, deoxyguanosine monophosphate and guanosine monophosphate. Comparison with related purine riboswitch structures reveals that the dG riboswitch achieves its specificity through modification of key interactions involving the nucleobase and rearrangement of the ligand-binding pocket to accommodate the additional sugar moiety. In addition, we observe new conformational changes beyond the junctional binding pocket extending as far as peripheral loop-loop interactions. It appears that re-engineering riboswitch scaffolds will require consideration of selectivity features dispersed throughout the riboswitch tertiary fold, and structure-guided drug design efforts targeted to junctional RNA scaffolds need to be addressed within such an expanded framework.

-	Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.,Pikovskaya O, Polonskaia A, Patel DJ, Serganov A Nat Chem Biol. 2011 Aug 14;7(10):748-55. doi: 10.1038/nchembio.631. PMID:21841796<ref>PMID:21841796</ref>	+	==See Also==
-		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3skt" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Patel, D J~~]]	+	[[Category: Mesoplasma florum]]
-	[[Category: ~~Pikovskaya, O~~]]	+	[[Category: Patel DJ]]
-	[[Category: ~~Polonskaia, A~~]]	+	[[Category: Pikovskaya O]]
-	[[Category: ~~Serganov,~~ A]]	+	[[Category: Polonskaia A]]
-	[[Category: ~~2'-deoxy-guanosine]]~~	+	[[Category: Serganov A]]
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Three-way junction~~]]	+

OCA at 08:00, 29 June 2022

OCA — Wed, 29 Jun 2022 08:00:18 GMT

←Older revision		Revision as of 08:00, 29 June 2022
Line 1:		Line 1:

	==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak==		==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak==
-	<StructureSection load='3skt' size='340' side='right' caption='[[3skt]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='3skt' size='340' side='right'caption='[[3skt]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3SKT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SKT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]</div></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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [~~http~~://pdbe.org/3skt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3skt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3skt 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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [https://pdbe.org/3skt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [https://www.ebi.ac.uk/pdbsum/3skt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3skt ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Patel, D J]]		[[Category: Patel, D J]]
	[[Category: Pikovskaya, O]]		[[Category: Pikovskaya, O]]

OCA at 08:49, 11 August 2016

OCA — Thu, 11 Aug 2016 08:49:54 GMT

←Older revision		Revision as of 08:49, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak==		==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak==
	<StructureSection load='3skt' size='340' side='right' caption='[[3skt]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3skt' size='340' side='right' caption='[[3skt]], [[Resolution\|resolution]] 3.10Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]</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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [http://www.ebi.ac.uk/pdbsum/3skt 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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [http://pdbe.org/3skt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [http://www.ebi.ac.uk/pdbsum/3skt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3skt ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3skt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:00, 4 January 2015

OCA — Sun, 04 Jan 2015 11:00:42 GMT

←Older revision		Revision as of 11:00, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]</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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [http://www.ebi.ac.uk/pdbsum/3skt 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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [http://www.ebi.ac.uk/pdbsum/3skt 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 14:		Line 14:
	Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.,Pikovskaya O, Polonskaia A, Patel DJ, Serganov A Nat Chem Biol. 2011 Aug 14;7(10):748-55. doi: 10.1038/nchembio.631. PMID:21841796<ref>PMID:21841796</ref>		Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.,Pikovskaya O, Polonskaia A, Patel DJ, Serganov A Nat Chem Biol. 2011 Aug 14;7(10):748-55. doi: 10.1038/nchembio.631. PMID:21841796<ref>PMID:21841796</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Patel, D J.]]	+	[[Category: Patel, D J]]
-	[[Category: Pikovskaya, O.]]	+	[[Category: Pikovskaya, O]]
-	[[Category: Polonskaia, A.]]	+	[[Category: Polonskaia, A]]
-	[[Category: Serganov, A.]]	+	[[Category: Serganov, A]]
	[[Category: 2'-deoxy-guanosine]]		[[Category: 2'-deoxy-guanosine]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Three-way junction]]		[[Category: Three-way junction]]

OCA at 05:26, 5 June 2014

OCA — Thu, 05 Jun 2014 05:26:55 GMT

←Older revision		Revision as of 05:26, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3skt.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak==
		+	<StructureSection load='3skt' size='340' side='right' caption='[[3skt]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3skl\|3skl]], [[3skr\|3skr]], [[3skw\|3skw]], [[3skz\|3skz]]</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=3skt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skt RCSB], [http://www.ebi.ac.uk/pdbsum/3skt PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Purine riboswitches have an essential role in genetic regulation of bacterial metabolism. This family includes the 2'-deoxyguanosine (dG) riboswitch, which is involved in feedback control of deoxyguanosine biosynthesis. To understand the principles that define dG selectivity, we determined crystal structures of the natural Mesoplasma florum riboswitch bound to cognate dG as well as to noncognate guanosine, deoxyguanosine monophosphate and guanosine monophosphate. Comparison with related purine riboswitch structures reveals that the dG riboswitch achieves its specificity through modification of key interactions involving the nucleobase and rearrangement of the ligand-binding pocket to accommodate the additional sugar moiety. In addition, we observe new conformational changes beyond the junctional binding pocket extending as far as peripheral loop-loop interactions. It appears that re-engineering riboswitch scaffolds will require consideration of selectivity features dispersed throughout the riboswitch tertiary fold, and structure-guided drug design efforts targeted to junctional RNA scaffolds need to be addressed within such an expanded framework.

-	<!--	+	Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.,Pikovskaya O, Polonskaia A, Patel DJ, Serganov A Nat Chem Biol. 2011 Aug 14;7(10):748-55. doi: 10.1038/nchembio.631. PMID:21841796<ref>PMID:21841796</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3skt"~~, ~~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_3skt\| PDB=3skt \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the ~~2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21841796}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21841796 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21841796}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021841796<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Patel, D J.]]		[[Category: Patel, D J.]]
	[[Category: Pikovskaya, O.]]		[[Category: Pikovskaya, O.]]

OCA at 08:02, 30 October 2011

OCA — Sun, 30 Oct 2011 08:02:52 GMT

←Older revision		Revision as of 08:02, 30 October 2011
Line 1:		Line 1:
-	[[Image:3skt.~~jpg~~\|left\|200px]]	+	[[Image:3skt.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak===		===Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21841796}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21841796 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21841796}}

	==About this Structure==		==About this Structure==
	[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA].		[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021841796</ref><references group="xtra"/>
	[[Category: Patel, D J.]]		[[Category: Patel, D J.]]
	[[Category: Pikovskaya, O.]]		[[Category: Pikovskaya, O.]]

OCA at 06:31, 17 August 2011

OCA — Wed, 17 Aug 2011 06:31:34 GMT

←Older revision		Revision as of 06:31, 17 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3skt.jpg\|left\|200px]]

-	The ~~entry 3skt~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3skt", 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_3skt\| PDB=3skt \| SCENE= }}

-	~~Authors: Pikovskaya~~, ~~O., Polonskaia, A., Patel, D.J., Serganov, A.~~	+	===Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak===

-	~~Description: Crystal structure of the~~ 2'-~~Deoxyguanosine riboswitch bound to~~ 2'-~~Deoxyguanosine, manganese Soak~~	+
		+	==About this Structure==
		+	[[3skt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKT OCA].
		+	[[Category: Patel, D J.]]
		+	[[Category: Pikovskaya, O.]]
		+	[[Category: Polonskaia, A.]]
		+	[[Category: Serganov, A.]]
		+	[[Category: 2'-deoxy-guanosine]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]
		+	[[Category: Three-way junction]]

OCA at 05:39, 27 July 2011

OCA — Wed, 27 Jul 2011 05:39:44 GMT

←Older revision		Revision as of 05:39, 27 July 2011
Line 5:		Line 5:
	Authors: Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.		Authors: Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.

-	Description: Crystal structure of the riboswitch bound to ~~ligand 1~~, manganese ~~soak~~	+	Description: Crystal structure of the 2'-Deoxyguanosine riboswitch bound to 2'-Deoxyguanosine, manganese Soak

OCA at 06:52, 13 July 2011

OCA — Wed, 13 Jul 2011 06:52:07 GMT

←Older revision		Revision as of 06:52, 13 July 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3skt is ON HOLD	+	The entry 3skt is ON HOLD until Paper Publication

	Authors: Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.		Authors: Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.

	Description: Crystal structure of the riboswitch bound to ligand 1, manganese soak		Description: Crystal structure of the riboswitch bound to ligand 1, manganese soak

OCA: Protected "3skt" [edit=sysop:move=sysop]

OCA — Wed, 29 Jun 2011 05:48:31 GMT

Protected "3skt" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:48, 29 June 2011