2d3d - Revision history

OCA at 13:46, 13 March 2024

2024-03-13T13:46:05Z

← Older revision		Revision as of 13:46, 13 March 2024
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	<StructureSection load='2d3d' size='340' side='right'caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d3d' size='340' side='right'caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3D FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.6Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Vts1 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [https://pdbe.org/2d3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [https://www.ebi.ac.uk/pdbsum/2d3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3d 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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [https://pdbe.org/2d3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [https://www.ebi.ac.uk/pdbsum/2d3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3d ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/VTS1_YEAST VTS1_YEAST] RNA-binding protein involved in post-transcriptional regulation through transcript degradation of SRE (SMG-recognition elements) bearing mRNAs. May be involved in vacuolar protein transport.<ref>PMID:11445562</ref> <ref>PMID:12858164</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=2d3d 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=2d3d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1 has a high affinity towards RNA hairpins containing a CUGGC pentaloop. We present the 1.6 Angstroms X-ray crystal structure of the Vts1 SAM domain in its unliganded state, and the NMR solution structure of this domain in its RNA-bound state. Both structures reveal a canonical five helix SAM domain flanked by additional secondary structural elements at the N and C termini. The two structures are essentially identical, implying that no major structural rearrangements occur upon RNA binding. Amide chemical shift changes map the RNA-binding site to a shallow, basic patch at the junction of helix alpha5 and the loop connecting helices alpha1 and alpha2.

	The NMR and X-ray structures of the Saccharomyces cerevisiae Vts1 SAM domain define a surface for the recognition of RNA hairpins.,Aviv T, Amborski AN, Zhao XS, Kwan JJ, Johnson PE, Sicheri F, Donaldson LW J Mol Biol. 2006 Feb 17;356(2):274-9. Epub 2005 Dec 7. PMID:16375924<ref>PMID:16375924</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2d3d" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Atcc 18824]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Amborski~~, A N~~]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Aviv, T]]		[[Category: Amborski AN]]
	[[Category: Donaldson~~, L W~~]]		[[Category: Aviv T]]
	[[Category: Johnson~~, P E~~]]		[[Category: Donaldson LW]]
	[[Category: Kwan~~, J J~~]]		[[Category: Johnson PE]]
	[[Category: Sicheri, F]]		[[Category: Kwan JJ]]
	[[Category: Zhao~~, X S]]~~		[[Category: Sicheri F]]
	~~[[Category: Rna binding]]~~		[[Category: Zhao XS]]
	~~[[Category: Rna binding protein]]~~
	~~[[Category: Sam domain]]~~
	~~[[Category: Sre hairpin binding~~]]

OCA at 11:53, 3 February 2021

2021-02-03T11:53:52Z

← Older revision		Revision as of 11:53, 3 February 2021
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	==crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1==		==crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1==
	<StructureSection load='2d3d' size='340' side='right' caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d3d' size='340' side='right'caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D3D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [~~http~~://pdbe.org/2d3d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d3d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3d 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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [https://pdbe.org/2d3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [https://www.ebi.ac.uk/pdbsum/2d3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
			[[Category: Large Structures]]
	[[Category: Amborski, A N]]		[[Category: Amborski, A N]]
	[[Category: Aviv, T]]		[[Category: Aviv, T]]

OCA at 06:42, 30 May 2018

2018-05-30T06:42:45Z

← Older revision		Revision as of 06:42, 30 May 2018
Line 1:		Line 1:

	==crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1==		==crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1==
	<StructureSection load='2d3d' size='340' side='right' caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d3d' size='340' side='right' caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [http://pdbe.org/2d3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [http://www.ebi.ac.uk/pdbsum/2d3d 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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [http://pdbe.org/2d3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [http://www.ebi.ac.uk/pdbsum/2d3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3d_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>

OCA at 19:23, 7 February 2016

2016-02-07T19:23:54Z

← Older revision		Revision as of 19:23, 7 February 2016
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	<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=2d3d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:20, 10 September 2015

2015-09-10T04:20:40Z

← Older revision		Revision as of 04:20, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2d3d' size='340' side='right' caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2d3d' size='340' side='right' caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [http://www.ebi.ac.uk/pdbsum/2d3d 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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [http://pdbe.org/2d3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [http://www.ebi.ac.uk/pdbsum/2d3d PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2d3d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Saccharomyces cerevisiae~~]]		[[Category: Atcc 18824]]
	[[Category: Amborski, A N]]		[[Category: Amborski, A N]]
	[[Category: Aviv, T]]		[[Category: Aviv, T]]

OCA at 16:58, 15 January 2015

2015-01-15T16:58:28Z

← Older revision		Revision as of 16:58, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [http://www.ebi.ac.uk/pdbsum/2d3d 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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [http://www.ebi.ac.uk/pdbsum/2d3d PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Amborski, A N.]]		[[Category: Amborski, A N]]
	[[Category: Aviv, T.]]		[[Category: Aviv, T]]
	[[Category: Donaldson, L W.]]		[[Category: Donaldson, L W]]
	[[Category: Johnson, P E.]]		[[Category: Johnson, P E]]
	[[Category: Kwan, J J.]]		[[Category: Kwan, J J]]
	[[Category: Sicheri, F.]]		[[Category: Sicheri, F]]
	[[Category: Zhao, X S.]]		[[Category: Zhao, X S]]
	[[Category: Rna binding]]		[[Category: Rna binding]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]
	[[Category: Sam domain]]		[[Category: Sam domain]]
	[[Category: Sre hairpin binding]]		[[Category: Sre hairpin binding]]

OCA at 00:24, 30 September 2014

2014-09-30T00:24:19Z

← Older revision		Revision as of 00:24, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2d3d~~.~~png~~\|~~left~~\|~~200px~~]]		==crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1==
			<StructureSection load='2d3d' size='340' side='right' caption='[[2d3d]], [[Resolution\|resolution]] 1.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [http://www.ebi.ac.uk/pdbsum/2d3d 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/d3/2d3d_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 SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1 has a high affinity towards RNA hairpins containing a CUGGC pentaloop. We present the 1.6 Angstroms X-ray crystal structure of the Vts1 SAM domain in its unliganded state, and the NMR solution structure of this domain in its RNA-bound state. Both structures reveal a canonical five helix SAM domain flanked by additional secondary structural elements at the N and C termini. The two structures are essentially identical, implying that no major structural rearrangements occur upon RNA binding. Amide chemical shift changes map the RNA-binding site to a shallow, basic patch at the junction of helix alpha5 and the loop connecting helices alpha1 and alpha2.

	~~{{STRUCTURE_2d3d\| PDB=2d3d \| SCENE= }}~~		The NMR and X-ray structures of the Saccharomyces cerevisiae Vts1 SAM domain define a surface for the recognition of RNA hairpins.,Aviv T, Amborski AN, Zhao XS, Kwan JJ, Johnson PE, Sicheri F, Donaldson LW J Mol Biol. 2006 Feb 17;356(2):274-9. Epub 2005 Dec 7. PMID:16375924<ref>PMID:16375924</ref>

	~~===crystal structure~~ of the ~~RNA binding SAM domain of saccharomyces cerevisiae Vts1===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16375924}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2d3d]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016375924<~~/~~ref~~><~~ref group="xtra">PMID:012858164</ref><references group="xtra"~~/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Amborski, A N.]]		[[Category: Amborski, A N.]]

OCA at 12:23, 23 January 2013

2013-01-23T12:23:27Z

← Older revision		Revision as of 12:23, 23 January 2013
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	[[Image:2d3d.png\|left\|200px]]		[[Image:2d3d.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2d3d", 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_2d3d\| PDB=2d3d \| SCENE= }}		{{STRUCTURE_2d3d\| PDB=2d3d \| SCENE= }}

	===crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1===		===crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16375924}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16375924 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16375924}}		{{ABSTRACT_PUBMED_16375924}}

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	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16375924~~</ref><ref group="xtra">PMID:~~12858164~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016375924</ref><ref group="xtra">PMID:012858164</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Amborski, A N.]]		[[Category: Amborski, A N.]]

OCA: Protected "2d3d" [edit=sysop:move=sysop]

2011-03-14T19:02:29Z

Protected "2d3d" [edit=sysop:move=sysop]

← Older revision	Revision as of 19:02, 14 March 2011
(No difference)

OCA at 19:02, 14 March 2011

2011-03-14T19:02:27Z

← Older revision		Revision as of 19:02, 14 March 2011
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	~~{{Seed}}~~
	[[Image:2d3d.png\|left\|200px]]		[[Image:2d3d.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
	~~2D3D~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA].		[[2d3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA].

	==Reference==		==Reference==
Line 33:		Line 32:
	[[Category: Zhao, X S.]]		[[Category: Zhao, X S.]]
	[[Category: Rna binding]]		[[Category: Rna binding]]
			[[Category: Rna binding protein]]
	[[Category: Sam domain]]		[[Category: Sam domain]]
	[[Category: Sre hairpin binding]]		[[Category: Sre hairpin binding]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:00:00 2009''~~