3ucz - Revision history

OCA at 13:55, 14 March 2024

OCA — Thu, 14 Mar 2024 13:55:07 GMT

←Older revision		Revision as of 13:55, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3ucz' size='340' side='right'caption='[[3ucz]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3ucz' size='340' side='right'caption='[[3ucz]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ucz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UCZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ucz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UCZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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;~~'>~~[[3ucu\|3ucu]], [[3ud3\|3ud3]], [[3ud4\|3ud4]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [https://pdbe.org/3ucz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [https://www.ebi.ac.uk/pdbsum/3ucz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ucz 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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [https://pdbe.org/3ucz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [https://www.ebi.ac.uk/pdbsum/3ucz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ucz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>	+	[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacterial signaling pathway. The breakdown of c-di-GMP in the cell is accomplished enzymatically and results in the linear dinucleotide pGpG. The c-di-GMP-binding riboswitches must be able to discriminate between their cognate cyclic ligand and linear dinucleotides in order to be selective biological switches. It has been reported that the c-di-GMP-I riboswitch binds c-di-GMP five orders of magnitude better than the linear pGpG, but the cause of this large energetic difference in binding is unknown. Here we report binding data and crystal structures of several linear c-di-GMP analogs in complex with the c-di-GMP-I riboswitch. These data reveal the parameters for phosphate recognition and the structural basis of linear dinucleotide binding to the riboswitch. Additionally, the pH dependence of binding shows that exclusion of pGpG is not due to the additional negative charge on the ligand. These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogs with properties desirable for use as chemical tools and potential therapeutics.	+
-		+
-	Structural and biochemical characterization of linear dinucleotide analogs bound to the c-di-GMP-I aptamer.,Smith KD, Lipchock SV, Strobel SA Biochemistry. 2011 Dec 8. PMID:22148472<ref>PMID:22148472</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3ucz" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]		*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Smith, K D~~]]	+	[[Category: Vibrio cholerae]]
-	[[Category: ~~Strobel, S A~~]]	+	[[Category: Smith KD]]
-	[[Category: ~~Riboswitch]]~~	+	[[Category: Strobel SA]]
-	~~[[Category: Signaling protein-rna complex~~]]	+

OCA at 06:08, 13 July 2022

OCA — Wed, 13 Jul 2022 06:08:17 GMT

←Older revision		Revision as of 06:08, 13 July 2022
Line 1:		Line 1:

	==The c-di-GMP-I riboswitch bound to GpG==		==The c-di-GMP-I riboswitch bound to GpG==
-	<StructureSection load='3ucz' size='340' side='right' caption='[[3ucz]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='3ucz' size='340' side='right'caption='[[3ucz]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ucz]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UCZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ucz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UCZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ucu\|3ucu]], [[3ud3\|3ud3]], [[3ud4\|3ud4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ucu\|3ucu]], [[3ud3\|3ud3]], [[3ud4\|3ud4]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [~~http~~://pdbe.org/3ucz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ucz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ucz 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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [https://pdbe.org/3ucz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [https://www.ebi.ac.uk/pdbsum/3ucz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ucz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>	+	[[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Nucleoprotein\|Nucleoprotein]]	+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Smith, K D]]		[[Category: Smith, K D]]
	[[Category: Strobel, S A]]		[[Category: Strobel, S A]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Signaling protein-rna complex]]		[[Category: Signaling protein-rna complex]]

OCA at 11:29, 4 August 2016

OCA — Thu, 04 Aug 2016 11:29:22 GMT

←Older revision		Revision as of 11:29, 4 August 2016
Line 1:		Line 1:
		+
	==The c-di-GMP-I riboswitch bound to GpG==		==The c-di-GMP-I riboswitch bound to GpG==
	<StructureSection load='3ucz' size='340' side='right' caption='[[3ucz]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3ucz' size='340' side='right' caption='[[3ucz]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ucz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UCZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ucz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UCZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ucu\|3ucu]], [[3ud3\|3ud3]], [[3ud4\|3ud4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ucu\|3ucu]], [[3ud3\|3ud3]], [[3ud4\|3ud4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [http://www.ebi.ac.uk/pdbsum/3ucz 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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [http://pdbe.org/3ucz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [http://www.ebi.ac.uk/pdbsum/3ucz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ucz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3ucz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Smith, K D]]		[[Category: Smith, K D]]
	[[Category: Strobel, S A]]		[[Category: Strobel, S A]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Signaling protein-rna complex]]		[[Category: Signaling protein-rna complex]]

OCA at 13:54, 24 December 2014

OCA — Wed, 24 Dec 2014 13:54:32 GMT

←Older revision		Revision as of 13:54, 24 December 2014
Line 9:		Line 9:
	<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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [http://www.ebi.ac.uk/pdbsum/3ucz 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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [http://www.ebi.ac.uk/pdbsum/3ucz PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 17:11, 9 December 2014

OCA — Tue, 09 Dec 2014 17:11:37 GMT

←Older revision		Revision as of 17:11, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3ucz.~~png~~\|~~left~~\|~~200px~~]]	+	==The c-di-GMP-I riboswitch bound to GpG==
		+	<StructureSection load='3ucz' size='340' side='right' caption='[[3ucz]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ucz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UCZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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">[[3ucu\|3ucu]], [[3ud3\|3ud3]], [[3ud4\|3ud4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ucz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ucz RCSB], [http://www.ebi.ac.uk/pdbsum/3ucz PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacterial signaling pathway. The breakdown of c-di-GMP in the cell is accomplished enzymatically and results in the linear dinucleotide pGpG. The c-di-GMP-binding riboswitches must be able to discriminate between their cognate cyclic ligand and linear dinucleotides in order to be selective biological switches. It has been reported that the c-di-GMP-I riboswitch binds c-di-GMP five orders of magnitude better than the linear pGpG, but the cause of this large energetic difference in binding is unknown. Here we report binding data and crystal structures of several linear c-di-GMP analogs in complex with the c-di-GMP-I riboswitch. These data reveal the parameters for phosphate recognition and the structural basis of linear dinucleotide binding to the riboswitch. Additionally, the pH dependence of binding shows that exclusion of pGpG is not due to the additional negative charge on the ligand. These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogs with properties desirable for use as chemical tools and potential therapeutics.

-	~~{{STRUCTURE_3ucz\| PDB=3ucz \| SCENE= }}~~	+	Structural and biochemical characterization of linear dinucleotide analogs bound to the c-di-GMP-I aptamer.,Smith KD, Lipchock SV, Strobel SA Biochemistry. 2011 Dec 8. PMID:22148472<ref>PMID:22148472</ref>

-	~~===The c-di-GMP-I riboswitch bound to GpG===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22148472}}~~	+	==See Also==
-		+	*[[Nucleoprotein\|Nucleoprotein]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3ucz~~]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:022148472<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Smith, K D.]]	+	[[Category: Smith, K D]]
-	[[Category: Strobel, S A.]]	+	[[Category: Strobel, S A]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Signaling protein-rna complex]]		[[Category: Signaling protein-rna complex]]

OCA at 05:52, 17 October 2012

OCA — Wed, 17 Oct 2012 05:52:29 GMT

←Older revision		Revision as of 05:52, 17 October 2012
Line 1:		Line 1:
-	[[Image:3ucz.~~jpg~~\|left\|200px]]	+	[[Image:3ucz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ucz", 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_3ucz\| PDB=3ucz \| SCENE= }}		{{STRUCTURE_3ucz\| PDB=3ucz \| SCENE= }}

	===The c-di-GMP-I riboswitch bound to GpG===		===The c-di-GMP-I riboswitch bound to GpG===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22148472}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22148472 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22148472}}		{{ABSTRACT_PUBMED_22148472}}

OCA at 06:03, 4 January 2012

OCA — Wed, 04 Jan 2012 06:03:09 GMT

←Older revision		Revision as of 06:03, 4 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ucz.jpg\|left\|200px]]

-	The ~~entry 3ucz~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ucz", 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_3ucz\| PDB=3ucz \| SCENE= }}

-	~~Authors: Smith, K.D., Strobel, S.A.~~	+	===The c-di-GMP-I riboswitch bound to GpG===

-	~~Description:~~ The c-di-~~GMP~~-~~I riboswitch bound to GpG~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22148472}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22148472 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22148472}}
		+
		+	==About this Structure==
		+	[[3ucz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UCZ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022148472</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Smith, K D.]]
		+	[[Category: Strobel, S A.]]
		+	[[Category: Riboswitch]]
		+	[[Category: Signaling protein-rna complex]]

OCA at 11:52, 16 November 2011

OCA — Wed, 16 Nov 2011 11:52:06 GMT

←Older revision		Revision as of 11:52, 16 November 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Smith, K.D., Strobel, S.A.		Authors: Smith, K.D., Strobel, S.A.

	Description: The c-di-GMP-I riboswitch bound to GpG		Description: The c-di-GMP-I riboswitch bound to GpG

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

OCA — Wed, 02 Nov 2011 08:02:07 GMT

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

←Older revision

Revision as of 08:02, 2 November 2011

OCA: New page: '''Unreleased structure''' The entry 3ucz is ON HOLD Authors: Smith, K.D., Strobel, S.A. Description: The c-di-GMP-I riboswitch bound to GpG

OCA — Wed, 02 Nov 2011 08:02:06 GMT

New page: '''Unreleased structure''' The entry 3ucz is ON HOLD Authors: Smith, K.D., Strobel, S.A. Description: The c-di-GMP-I riboswitch bound to GpG

New page

'''Unreleased structure'''

The entry 3ucz is ON HOLD

Authors: Smith, K.D., Strobel, S.A.

Description: The c-di-GMP-I riboswitch bound to GpG