5vjb - Revision history

OCA at 14:10, 13 March 2024

OCA — Wed, 13 Mar 2024 14:10:48 GMT

←Older revision		Revision as of 14:10, 13 March 2024
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	<StructureSection load='5vjb' size='340' side='right'caption='[[5vjb]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5vjb' size='340' side='right'caption='[[5vjb]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vjb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VJB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vjb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VJB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GAI:GUANIDINE'>GAI</scene~~>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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]] 2.1Å</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='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=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
-	<~~tr id~~='~~related~~'><~~td class="sblockLbl"~~><~~b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5vj9\|5vj9]]~~</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=5vjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjb OCA], [https://pdbe.org/5vjb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vjb RCSB], [https://www.ebi.ac.uk/pdbsum/5vjb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjb ProSAT]</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=5vjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjb OCA], [~~http~~://pdbe.org/5vjb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vjb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vjb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjb ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The guanidine-II riboswitch, also known as mini-ykkC, is a conserved mRNA element with more than 800 examples in bacteria. It consists of two stem-loops capped by identical, conserved tetraloops that are separated by a linker region of variable length and sequence. Like the guanidine-I riboswitch, it controls the expression of guanidine carboxylases and SugE-like genes. The guanidine-II riboswitch specifically binds free guanidinium cations and functions as a translationally controlled on-switch. Here we report the structure of a P2 stem-loop from the Pseudomonas aeruginosa guanidine-II riboswitch aptamer bound to guanidine at 1.57 A resolution. The hairpins dimerize via the conserved tetraloop, which also contains the binding pocket. Two guanidinium molecules bind near the dimerization interface, one in each tetraloop. The guanidinium cation is engaged in extensive hydrogen bonding to the RNA. Contacts include the Hoogsteen face of a guanine base and three nonbridging phosphate oxygens. Cation-pi interactions and ionic interactions also stabilize ligand binding. The guanidine-II riboswitch utilizes the same recognition strategies as the guanidine-I riboswitch while adopting an entirely different and much smaller RNA fold.
-
-	Structural basis for ligand binding to the guanidine-II riboswitch.,Reiss CW, Strobel SA RNA. 2017 Sep;23(9):1338-1343. doi: 10.1261/rna.061804.117. Epub 2017 Jun 9. PMID:28600356<ref>PMID:28600356</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5vjb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]		*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Reiss, C W~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Strobel, S A~~]]	+	[[Category: Reiss CW]]
-	[[Category: ~~Guanidine]]~~	+	[[Category: Strobel SA]]
-	~~[[Category: Hairpin]]~~	+
-	~~[[Category: Kissing loop]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 09:35, 1 January 2020

OCA — Wed, 01 Jan 2020 09:35:27 GMT

←Older revision		Revision as of 09:35, 1 January 2020
Line 1:		Line 1:

	==Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa==		==Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa==
-	<StructureSection load='5vjb' size='340' side='right' caption='[[5vjb]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5vjb' size='340' side='right'caption='[[5vjb]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vjb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vjb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJB FirstGlance]. <br>
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Riboswitch\|Riboswitch]]	+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Reiss, C W]]		[[Category: Reiss, C W]]
	[[Category: Strobel, S A]]		[[Category: Strobel, S A]]

OCA at 08:33, 6 October 2017

OCA — Fri, 06 Oct 2017 08:33:24 GMT

←Older revision		Revision as of 08:33, 6 October 2017
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5vjb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vjb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch\|Riboswitch]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:54, 30 August 2017

OCA — Wed, 30 Aug 2017 03:54:29 GMT

←Older revision		Revision as of 03:54, 30 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vjb is ~~ON HOLD~~	+	==Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa==
		+	<StructureSection load='5vjb' size='340' side='right' caption='[[5vjb]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vjb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vj9\|5vj9]]</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=5vjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjb OCA], [http://pdbe.org/5vjb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjb RCSB], [http://www.ebi.ac.uk/pdbsum/5vjb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjb ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The guanidine-II riboswitch, also known as mini-ykkC, is a conserved mRNA element with more than 800 examples in bacteria. It consists of two stem-loops capped by identical, conserved tetraloops that are separated by a linker region of variable length and sequence. Like the guanidine-I riboswitch, it controls the expression of guanidine carboxylases and SugE-like genes. The guanidine-II riboswitch specifically binds free guanidinium cations and functions as a translationally controlled on-switch. Here we report the structure of a P2 stem-loop from the Pseudomonas aeruginosa guanidine-II riboswitch aptamer bound to guanidine at 1.57 A resolution. The hairpins dimerize via the conserved tetraloop, which also contains the binding pocket. Two guanidinium molecules bind near the dimerization interface, one in each tetraloop. The guanidinium cation is engaged in extensive hydrogen bonding to the RNA. Contacts include the Hoogsteen face of a guanine base and three nonbridging phosphate oxygens. Cation-pi interactions and ionic interactions also stabilize ligand binding. The guanidine-II riboswitch utilizes the same recognition strategies as the guanidine-I riboswitch while adopting an entirely different and much smaller RNA fold.

-	~~Authors~~:	+	Structural basis for ligand binding to the guanidine-II riboswitch.,Reiss CW, Strobel SA RNA. 2017 Sep;23(9):1338-1343. doi: 10.1261/rna.061804.117. Epub 2017 Jun 9. PMID:28600356<ref>PMID:28600356</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vjb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Reiss, C W]]
		+	[[Category: Strobel, S A]]
		+	[[Category: Guanidine]]
		+	[[Category: Hairpin]]
		+	[[Category: Kissing loop]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]

OCA: Protected "5vjb" [edit=sysop:move=sysop]

OCA — Thu, 27 Apr 2017 12:21:22 GMT

Protected "5vjb" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:21, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vjb is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 27 Apr 2017 12:21:20 GMT

New page: '''Unreleased structure''' The entry 5vjb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vjb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]