3iwn - Revision history

OCA at 10:07, 21 February 2024

OCA — Wed, 21 Feb 2024 10:07:14 GMT

←Older revision		Revision as of 10:07, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3iwn' size='340' side='right'caption='[[3iwn]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='3iwn' size='340' side='right'caption='[[3iwn]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. The October 2010 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IWN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. The October 2010 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IWN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</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]] 3.2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA, U1A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [https://pdbe.org/3iwn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [https://www.ebi.ac.uk/pdbsum/3iwn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwn 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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [https://pdbe.org/3iwn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [https://www.ebi.ac.uk/pdbsum/3iwn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwn 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]]
Line 20:		Line 20:
	</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=3iwn 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=3iwn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The cyclic diguanylate (bis-(3'-5')-cyclic dimeric guanosine monophosphate, c-di-GMP) riboswitch is the first known example of a gene-regulatory RNA that binds a second messenger. c-di-GMP is widely used by bacteria to regulate processes ranging from biofilm formation to the expression of virulence genes. The cocrystal structure of the c-di-GMP responsive GEMM riboswitch upstream of the tfoX gene of Vibrio cholerae reveals the second messenger binding the RNA at a three-helix junction. The two-fold symmetric second messenger is recognized asymmetrically by the monomeric riboswitch using canonical and noncanonical base-pairing as well as intercalation. These interactions explain how the RNA discriminates against cyclic diadenylate (c-di-AMP), a putative bacterial second messenger. Small-angle X-ray scattering and biochemical analyses indicate that the RNA undergoes compaction and large-scale structural rearrangement in response to ligand binding, consistent with organization of the core three-helix junction of the riboswitch concomitant with binding of c-di-GMP.
-
-	Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.,Kulshina N, Baird NJ, Ferre-D'Amare AR Nat Struct Mol Biol. 2009 Dec;16(12):1212-7. Epub 2009 Nov 8. PMID:19898478<ref>PMID:19898478</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3iwn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Riboswitches]]		[[Category: Riboswitches]]
-	[[Category: ~~Amare, A R.Ferre-D~~]]	+	[[Category: Vibrio cholerae]]
-	[[Category: Baird~~, N J~~]]	+	[[Category: Baird NJ]]
-	[[Category: ~~Kulshina, N]]~~	+	[[Category: Ferre-D'Amare AR]]
-	~~[[Category: Acetylation]]~~	+	[[Category: Kulshina N]]
-	~~[[Category: Mrna processing]]~~	+
-	~~[[Category: Mrna splicing]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Ribonucleoprotein]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna~~-~~binding~~]]	+
-	[[Category: ~~Rna-rna binding protein complex]]~~	+
-	~~[[Category: Spliceosome]]~~	+
-	~~[[Category: U1a~~]]	+

OCA at 12:15, 13 October 2021

OCA — Wed, 13 Oct 2021 12:15:55 GMT

←Older revision		Revision as of 12:15, 13 October 2021
Line 1:		Line 1:

	==Co-crystal structure of a bacterial c-di-GMP riboswitch==		==Co-crystal structure of a bacterial c-di-GMP riboswitch==
-	<StructureSection load='3iwn' size='340' side='right' caption='[[3iwn]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='3iwn' size='340' side='right'caption='[[3iwn]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. The October 2010 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IWN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. The October 2010 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IWN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA, U1A ([~~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, U1A ([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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [~~http~~://pdbe.org/3iwn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3iwn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwn 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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [https://pdbe.org/3iwn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [https://www.ebi.ac.uk/pdbsum/3iwn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwn 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]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Nucleoprotein\|Nucleoprotein]]	+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
-	*[[Riboswitch\|Riboswitch]]	+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Riboswitches]]		[[Category: Riboswitches]]

OCA at 09:32, 19 December 2018

OCA — Wed, 19 Dec 2018 09:32:14 GMT

←Older revision		Revision as of 09:32, 19 December 2018
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IWN FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IWN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,~~3AS~~,5S,~~7AR~~,9R,10R,~~10AS~~,12S,~~14AR~~)-3,5,10,12-~~TETRAHYDROXY~~-5,12-~~DIOXIDOOCTAHYDRO~~-2H,7H-~~DIFURO~~[3,2-D 3,2-J][1,3,7,9,2,8]~~TETRAOXADIPHOSPHACYCLODODECINE~~-2,9-~~DIYL~~]~~BIS~~(2-~~AMINO~~-1,9-~~DIHYDRO~~-6H-~~PURIN~~-6-~~ONE~~)'>C2E</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA, U1A ([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, U1A ([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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [http://pdbe.org/3iwn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [http://www.ebi.ac.uk/pdbsum/3iwn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwn 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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [http://pdbe.org/3iwn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [http://www.ebi.ac.uk/pdbsum/3iwn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwn ProSAT]</span></td></tr>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iw/3iwn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iw/3iwn_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 43:		Line 43:
	[[Category: Baird, N J]]		[[Category: Baird, N J]]
	[[Category: Kulshina, N]]		[[Category: Kulshina, N]]
		+	[[Category: Acetylation]]
	[[Category: Mrna processing]]		[[Category: Mrna processing]]
	[[Category: Mrna splicing]]		[[Category: Mrna splicing]]

OCA at 17:15, 5 August 2016

OCA — Fri, 05 Aug 2016 17:15:01 GMT

←Older revision		Revision as of 17:15, 5 August 2016
Line 1:		Line 1:
		+
	==Co-crystal structure of a bacterial c-di-GMP riboswitch==		==Co-crystal structure of a bacterial c-di-GMP riboswitch==
	<StructureSection load='3iwn' size='340' side='right' caption='[[3iwn]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='3iwn' size='340' side='right' caption='[[3iwn]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IWN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IWN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA, U1A ([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, U1A ([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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [http://www.ebi.ac.uk/pdbsum/3iwn 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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [http://pdbe.org/3iwn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [http://www.ebi.ac.uk/pdbsum/3iwn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iwn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=3iwn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	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 3iwn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Riboswitches]]		[[Category: Riboswitches]]

OCA at 20:34, 25 December 2014

OCA — Thu, 25 Dec 2014 20:34:09 GMT

←Older revision		Revision as of 20:34, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3iwn~~\| ~~PDB~~=3iwn \| ~~SCENE~~= }}	+	==Co-crystal structure of a bacterial c-di-GMP riboswitch==
-	===Co-~~crystal~~ structure of a bacterial c-di-GMP ~~riboswitch===~~	+	<StructureSection load='3iwn' size='340' side='right' caption='[[3iwn]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19898478}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3iwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IWN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA, U1A ([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=3iwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iwn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iwn RCSB], [http://www.ebi.ac.uk/pdbsum/3iwn PDBsum]</span></td></tr>
		+	</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 ==
		+	[[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/iw/3iwn_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 cyclic diguanylate (bis-(3'-5')-cyclic dimeric guanosine monophosphate, c-di-GMP) riboswitch is the first known example of a gene-regulatory RNA that binds a second messenger. c-di-GMP is widely used by bacteria to regulate processes ranging from biofilm formation to the expression of virulence genes. The cocrystal structure of the c-di-GMP responsive GEMM riboswitch upstream of the tfoX gene of Vibrio cholerae reveals the second messenger binding the RNA at a three-helix junction. The two-fold symmetric second messenger is recognized asymmetrically by the monomeric riboswitch using canonical and noncanonical base-pairing as well as intercalation. These interactions explain how the RNA discriminates against cyclic diadenylate (c-di-AMP), a putative bacterial second messenger. Small-angle X-ray scattering and biochemical analyses indicate that the RNA undergoes compaction and large-scale structural rearrangement in response to ligand binding, consistent with organization of the core three-helix junction of the riboswitch concomitant with binding of c-di-GMP.

-	~~==About this Structure==~~	+	Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.,Kulshina N, Baird NJ, Ferre-D'Amare AR Nat Struct Mol Biol. 2009 Dec;16(12):1212-7. Epub 2009 Nov 8. PMID:19898478<ref>PMID:19898478</ref>
-	[[3iwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the ~~Month] feature on ''Riboswitches''~~ by ~~David Goodsell is [http://dx~~.~~doi~~.~~org/10~~.~~2210/rcsb_pdb/mom_2010_10 10~~.~~2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3IWN OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Nucleoprotein\|Nucleoprotein]]		*[[Nucleoprotein\|Nucleoprotein]]
	*[[Riboswitch\|Riboswitch]]		*[[Riboswitch\|Riboswitch]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019898478<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Riboswitches]]		[[Category: Riboswitches]]
-	[[Category: Amare, A R.Ferre-D.]]	+	[[Category: Amare, A R.Ferre-D]]
-	[[Category: Baird, N J.]]	+	[[Category: Baird, N J]]
-	[[Category: Kulshina, N.]]	+	[[Category: Kulshina, N]]
	[[Category: Mrna processing]]		[[Category: Mrna processing]]
	[[Category: Mrna splicing]]		[[Category: Mrna splicing]]

OCA at 10:53, 11 March 2013

OCA — Mon, 11 Mar 2013 10:53:26 GMT

←Older revision		Revision as of 10:53, 11 March 2013
Line 1:		Line 1:
-	[[Image:3iwn.png\|left\|200px]]
-
	{{STRUCTURE_3iwn\| PDB=3iwn \| SCENE= }}		{{STRUCTURE_3iwn\| PDB=3iwn \| SCENE= }}
-
	===Co-crystal structure of a bacterial c-di-GMP riboswitch===		===Co-crystal structure of a bacterial c-di-GMP riboswitch===
-
	{{ABSTRACT_PUBMED_19898478}}		{{ABSTRACT_PUBMED_19898478}}

OCA at 21:11, 20 October 2012

OCA — Sat, 20 Oct 2012 21:11:06 GMT

←Older revision		Revision as of 21:11, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3iwn]] is a 4 chain structure ~~of [[Nucleoprotein]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA].	+	[[3iwn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA].

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

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

OCA — Fri, 27 Jul 2012 12:48:14 GMT

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

←Older revision

Revision as of 12:48, 27 July 2012

OCA at 12:48, 27 July 2012

OCA — Fri, 27 Jul 2012 12:48:13 GMT

←Older revision		Revision as of 12:48, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3iwn.png\|left\|200px]]		[[Image:3iwn.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3iwn", 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_3iwn\| PDB=3iwn \| SCENE= }}		{{STRUCTURE_3iwn\| PDB=3iwn \| SCENE= }}

	===Co-crystal structure of a bacterial c-di-GMP riboswitch===		===Co-crystal structure of a bacterial c-di-GMP riboswitch===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19898478}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19898478 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19898478}}		{{ABSTRACT_PUBMED_19898478}}

	==About this Structure==		==About this Structure==
-	~~3IWN~~ is a 4 ~~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=3IWN OCA].	+	[[3iwn]] is a 4 chain structure of [[Nucleoprotein]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The October 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Riboswitches'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_10 10.2210/rcsb_pdb/mom_2010_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IWN OCA].
		+
		+	==See Also==
		+	*[[Nucleoprotein\|Nucleoprotein]]
		+	*[[Riboswitch\|Riboswitch]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19898478~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019898478</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: RCSB PDB Molecule of the Month]]
		+	[[Category: Riboswitches]]
	[[Category: Amare, A R.Ferre-D.]]		[[Category: Amare, A R.Ferre-D.]]
	[[Category: Baird, N J.]]		[[Category: Baird, N J.]]
	[[Category: Kulshina, N.]]		[[Category: Kulshina, N.]]
-	[[Category: Acetylation]]
	[[Category: Mrna processing]]		[[Category: Mrna processing]]
	[[Category: Mrna splicing]]		[[Category: Mrna splicing]]
Line 37:		Line 30:
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
-	[[Category: Rna/rna binding protein complex]]	+	[[Category: Rna-rna binding protein complex]]
	[[Category: Spliceosome]]		[[Category: Spliceosome]]
	[[Category: U1a]]		[[Category: U1a]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Dec 24 07:29:37 2009''

OCA at 05:29, 24 December 2009

OCA — Thu, 24 Dec 2009 05:29:38 GMT

←Older revision		Revision as of 05:29, 24 December 2009
Line 12:		Line 12:
	===Co-crystal structure of a bacterial c-di-GMP riboswitch===		===Co-crystal structure of a bacterial c-di-GMP riboswitch===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19898478}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19898478 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19898478}}

	==About this Structure==		==About this Structure==
Line 35:		Line 41:
	[[Category: U1a]]		[[Category: U1a]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed~~ Dec ~~23 08~~:58:06 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Dec 24 07:29:37 2009''