3g8s - Revision history

OCA at 09:53, 21 February 2024

OCA — Wed, 21 Feb 2024 09:53:02 GMT

←Older revision		Revision as of 09:53, 21 February 2024
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	<StructureSection load='3g8s' size='340' side='right'caption='[[3g8s]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3g8s' size='340' side='right'caption='[[3g8s]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g8s]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G8S 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]] 3.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <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;~~'>~~[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]~~</~~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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [https://pdbe.org/3g8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [https://www.ebi.ac.uk/pdbsum/3g8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8s 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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [https://pdbe.org/3g8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [https://www.ebi.ac.uk/pdbsum/3g8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8s 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g8s ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g8s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, much of the structural work to date has been done on a variant glmS ribozyme, derived from Thermoanaerobacter tengcongensis. Here we present structures of the B. anthracis glmS ribozyme in states before the activating sugar, glucosamine 6-phosphate (GlcN6P), has bound and after the reaction has occurred. These structures show an active site preorganized to bind GlcN6P that retains some affinity for the sugar even after cleavage of the RNA backbone. A structure of an inactive glmS ribozyme with a mutation distal from the ligand-binding pocket highlights a nucleotide critical to the reaction that does not affect GlcN6P binding. Structures of the glmS ribozyme bound to a naturally occurring inhibitor, glucose 6-phosphate (Glc6P), and a nonnatural activating sugar, mannosamine 6-phosphate (MaN6P), reveal a binding mode similar to that of GlcN6P. Kinetic analyses show a pH dependence of ligand binding that is consistent with titration of the cofactor's phosphate group and support a model in which the major determinant of activity is the sugar amine independent of its stereochemical presentation.
-
-	Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme.,Cochrane JC, Lipchock SV, Smith KD, Strobel SA Biochemistry. 2009 Apr 21;48(15):3239-46. PMID:19228039<ref>PMID:19228039</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3g8s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]		*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Bacillus anthracis]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cochrane~~, J C~~]]	+	[[Category: Cochrane JC]]
-	[[Category: Lipchock~~, S V~~]]	+	[[Category: Lipchock SV]]
-	[[Category: Smith~~, K D~~]]	+	[[Category: Smith KD]]
-	[[Category: Strobel~~, S A]]~~	+	[[Category: Strobel SA]]
-	~~[[Category: Catalytic rna]]~~	+
-	~~[[Category: Rna binding protein-rna complex~~]]	+

OCA at 20:03, 20 October 2021

OCA — Wed, 20 Oct 2021 20:03:31 GMT

←Older revision		Revision as of 20:03, 20 October 2021
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	==Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme==		==Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme==
-	<StructureSection load='3g8s' size='340' side='right' caption='[[3g8s]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='3g8s' size='340' side='right'caption='[[3g8s]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G8S 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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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">[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]</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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [~~http~~://pdbe.org/3g8s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g8s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8s 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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [https://pdbe.org/3g8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [https://www.ebi.ac.uk/pdbsum/3g8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8s 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g8/3g8s_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g8/3g8s_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:

	==See Also==		==See Also==
		+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cochrane, J C]]		[[Category: Cochrane, J C]]
	[[Category: Lipchock, S V]]		[[Category: Lipchock, S V]]

OCA at 07:00, 1 November 2017

OCA — Wed, 01 Nov 2017 07:00:11 GMT

←Older revision		Revision as of 07:00, 1 November 2017
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Nucleoprotein\|Nucleoprotein]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==

OCA at 08:29, 5 August 2016

OCA — Fri, 05 Aug 2016 08:29:36 GMT

←Older revision		Revision as of 08:29, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme==		==Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme==
	<StructureSection load='3g8s' size='340' side='right' caption='[[3g8s]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3g8s' size='340' side='right' caption='[[3g8s]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8S 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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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">[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]</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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [http://www.ebi.ac.uk/pdbsum/3g8s 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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [http://pdbe.org/3g8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [http://www.ebi.ac.uk/pdbsum/3g8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g8s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3g8s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cochrane, J C]]		[[Category: Cochrane, J C]]
	[[Category: Lipchock, S V]]		[[Category: Lipchock, S V]]

OCA at 17:16, 25 December 2014

OCA — Thu, 25 Dec 2014 17:16:28 GMT

←Older revision		Revision as of 17:16, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8S FirstGlance]. <br>		<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8S FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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">[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]</td></tr>
-	<tr><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 Homo sapiens])</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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [http://www.ebi.ac.uk/pdbsum/3g8s 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=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [http://www.ebi.ac.uk/pdbsum/3g8s 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cochrane, J C.]]	+	[[Category: Cochrane, J C]]
-	[[Category: Lipchock, S V.]]	+	[[Category: Lipchock, S V]]
-	[[Category: Smith, K D.]]	+	[[Category: Smith, K D]]
-	[[Category: Strobel, S A.]]	+	[[Category: Strobel, S A]]
	[[Category: Catalytic rna]]		[[Category: Catalytic rna]]
	[[Category: Rna binding protein-rna complex]]		[[Category: Rna binding protein-rna complex]]

OCA at 11:04, 29 September 2014

OCA — Mon, 29 Sep 2014 11:04:06 GMT

←Older revision		Revision as of 11:04, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3g8s.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme==
		+	<StructureSection load='3g8s' size='340' side='right' caption='[[3g8s]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g8s]] is a 12 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=3G8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8S FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</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">[[3g8t\|3g8t]], [[3g95\|3g95]], [[3g96\|3g96]], [[3g9c\|3g9c]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8s RCSB], [http://www.ebi.ac.uk/pdbsum/3g8s PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g8/3g8s_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, much of the structural work to date has been done on a variant glmS ribozyme, derived from Thermoanaerobacter tengcongensis. Here we present structures of the B. anthracis glmS ribozyme in states before the activating sugar, glucosamine 6-phosphate (GlcN6P), has bound and after the reaction has occurred. These structures show an active site preorganized to bind GlcN6P that retains some affinity for the sugar even after cleavage of the RNA backbone. A structure of an inactive glmS ribozyme with a mutation distal from the ligand-binding pocket highlights a nucleotide critical to the reaction that does not affect GlcN6P binding. Structures of the glmS ribozyme bound to a naturally occurring inhibitor, glucose 6-phosphate (Glc6P), and a nonnatural activating sugar, mannosamine 6-phosphate (MaN6P), reveal a binding mode similar to that of GlcN6P. Kinetic analyses show a pH dependence of ligand binding that is consistent with titration of the cofactor's phosphate group and support a model in which the major determinant of activity is the sugar amine independent of its stereochemical presentation.

-	~~{{STRUCTURE_3g8s\| PDB=3g8s \| SCENE= }}~~	+	Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme.,Cochrane JC, Lipchock SV, Smith KD, Strobel SA Biochemistry. 2009 Apr 21;48(15):3239-46. PMID:19228039<ref>PMID:19228039</ref>

-	~~===Crystal structure~~ of the ~~pre-cleaved Bacillus anthracis glmS ribozyme===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19228039}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3g8s]] is a 12 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=3G8S OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoprotein\|Nucleoprotein]]		*[[Nucleoprotein\|Nucleoprotein]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019228039<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cochrane, J C.]]		[[Category: Cochrane, J C.]]

OCA at 19:21, 20 October 2012

OCA — Sat, 20 Oct 2012 19:21:12 GMT

←Older revision		Revision as of 19:21, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3g8s]] is a 12 chain structure ~~of [[Nucleoprotein]] and [[Ribozyme]]~~ 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=3G8S OCA].	+	[[3g8s]] is a 12 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=3G8S OCA].

	==See Also==		==See Also==

OCA: Protected "3g8s" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 07:04:56 GMT

Protected "3g8s" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:04, 27 July 2012

OCA at 07:04, 27 July 2012

OCA — Fri, 27 Jul 2012 07:04:55 GMT

←Older revision		Revision as of 07:04, 27 July 2012
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-	{{Seed}}
	[[Image:3g8s.png\|left\|200px]]		[[Image:3g8s.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3g8s", 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),
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	{{STRUCTURE_3g8s\| PDB=3g8s \| SCENE= }}		{{STRUCTURE_3g8s\| PDB=3g8s \| SCENE= }}

	===Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme===		===Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19228039}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19228039 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19228039}}		{{ABSTRACT_PUBMED_19228039}}

	==About this Structure==		==About this Structure==
-	~~3G8S~~ is a 12 ~~chains~~ structure with ~~sequences~~ 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=3G8S OCA].	+	[[3g8s]] is a 12 chain structure of [[Nucleoprotein]] and [[Ribozyme]] 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=3G8S OCA].
		+
		+	==See Also==
		+	*[[Nucleoprotein\|Nucleoprotein]]
		+	*[[Ribozyme\|Ribozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19228039~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019228039</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cochrane, J C.]]		[[Category: Cochrane, J C.]]
Line 30:		Line 22:
	[[Category: Strobel, S A.]]		[[Category: Strobel, S A.]]
	[[Category: Catalytic rna]]		[[Category: Catalytic rna]]
-	[[Category: Rna binding protein/rna complex]]	+	[[Category: Rna binding protein-rna complex]]
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 15:06:25 2010''~~	+

OCA at 13:06, 28 January 2010

OCA — Thu, 28 Jan 2010 13:06:26 GMT

←Older revision		Revision as of 13:06, 28 January 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3g8s.~~jpg~~\|left\|200px]]	+	[[Image:3g8s.png\|left\|200px]]

	<!--		<!--
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3G8S is a 12 chains structure of sequences 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=3G8S OCA].	+	3G8S is a 12 chains structure with sequences 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=3G8S OCA].

	==Reference==		==Reference==
Line 32:		Line 32:
	[[Category: Rna binding protein/rna complex]]		[[Category: Rna binding protein/rna complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Nov 4 10~~:56:~~00 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 15:06:25 2010''