3i5y - Revision history

OCA at 07:38, 6 September 2023

OCA — Wed, 06 Sep 2023 07:38:42 GMT

←Older revision		Revision as of 07:38, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3i5y' size='340' side='right'caption='[[3i5y]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='3i5y' size='340' side='right'caption='[[3i5y]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~ADENYLATE+ESTER'>ANP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.49Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</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;~~'>~~[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">MSS116, YD9346.05C, YDR194C ([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'>[https://proteopedia.org/fgij/fg.htm?mol=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [https://pdbe.org/3i5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [https://www.ebi.ac.uk/pdbsum/3i5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5y 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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [https://pdbe.org/3i5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [https://www.ebi.ac.uk/pdbsum/3i5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST]] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>	+	[https://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Campo, M Del~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Lambowitz, A~~ M]]	+	[[Category: Del Campo M]]
-	[[Category: ~~Atp-binding]]~~	+	[[Category: Lambowitz AM]]
-	~~[[Category: Dead-box]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-rna complex]]~~	+
-	~~[[Category: Mitochondrion]]~~	+
-	~~[[Category: Mrna processing]]~~	+
-	~~[[Category: Mrna splicing]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Protein-rna complex]]~~	+
-	~~[[Category: Rna helicase]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Transit peptide]]~~	+
-	~~[[Category: Translation regulation~~]]	+

OCA at 10:58, 13 April 2022

OCA — Wed, 13 Apr 2022 10:58:35 GMT

←Older revision		Revision as of 10:58, 13 April 2022
Line 1:		Line 1:

	==Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP==		==Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP==
-	<StructureSection load='3i5y' size='340' side='right' caption='[[3i5y]], [[Resolution\|resolution]] 2.49Å' scene=''>	+	<StructureSection load='3i5y' size='340' side='right'caption='[[3i5y]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <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=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSS116, YD9346.05C, YDR194C ([~~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">MSS116, YD9346.05C, YDR194C ([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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [~~http~~://pdbe.org/3i5y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i5y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5y 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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [https://pdbe.org/3i5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [https://www.ebi.ac.uk/pdbsum/3i5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST]] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>	+	[[https://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST]] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Helicase\|Helicase]]	+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Campo, M Del]]		[[Category: Campo, M Del]]
	[[Category: Lambowitz, A M]]		[[Category: Lambowitz, A M]]

OCA at 09:44, 19 December 2018

OCA — Wed, 19 Dec 2018 09:44:43 GMT

←Older revision		Revision as of 09:44, 19 December 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/3i5y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/3i5y_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 14:52, 5 August 2016

OCA — Fri, 05 Aug 2016 14:52:22 GMT

←Older revision		Revision as of 14:52, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP==		==Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP==
	<StructureSection load='3i5y' size='340' side='right' caption='[[3i5y]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='3i5y' size='340' side='right' caption='[[3i5y]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <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=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSS116, YD9346.05C, YDR194C ([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">MSS116, YD9346.05C, YDR194C ([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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [http://www.ebi.ac.uk/pdbsum/3i5y 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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [http://pdbe.org/3i5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [http://www.ebi.ac.uk/pdbsum/3i5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5y 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=3i5y 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 3i5y" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Campo, M Del]]		[[Category: Campo, M Del]]
	[[Category: Lambowitz, A M]]		[[Category: Lambowitz, A M]]

OCA at 19:43, 25 December 2014

OCA — Thu, 25 Dec 2014 19:43:33 GMT

←Older revision		Revision as of 19:43, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <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=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSS116, YD9346.05C, YDR194C ([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">MSS116, YD9346.05C, YDR194C ([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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [http://www.ebi.ac.uk/pdbsum/3i5y 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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [http://www.ebi.ac.uk/pdbsum/3i5y PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST]] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Campo, M Del.]]	+	[[Category: Campo, M Del]]
-	[[Category: Lambowitz, A M.]]	+	[[Category: Lambowitz, A M]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Dead-box]]		[[Category: Dead-box]]

OCA at 13:10, 29 September 2014

OCA — Mon, 29 Sep 2014 13:10:50 GMT

←Older revision		Revision as of 13:10, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3i5y.~~png~~\|~~left~~\|200px]]	+	==Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP==
		+	<StructureSection load='3i5y' size='340' side='right' caption='[[3i5y]], [[Resolution\|resolution]] 2.49Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i5y]] is a 2 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=3I5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <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=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5x\|3i5x]], [[3i61\|3i61]], [[3i62\|3i62]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSS116, YD9346.05C, YDR194C ([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=3i5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5y RCSB], [http://www.ebi.ac.uk/pdbsum/3i5y 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/i5/3i5y_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 yeast DEAD box protein Mss116p is a general RNA chaperone that functions in mitochondrial group I and II intron splicing, translational activation, and RNA end processing. Here we determined high-resolution X-ray crystal structures of Mss116p complexed with an RNA oligonucleotide and ATP analogs AMP-PNP, ADP-BeF(3)(-), or ADP-AlF(4)(-). The structures show the entire helicase core acting together with a functionally important C-terminal extension. In all structures, the helicase core is in a closed conformation with a wedge alpha helix bending RNA 3' of the central bound nucleotides, as in previous DEAD box protein structures. Notably, Mss116p's C-terminal extension also bends RNA 5' of the central nucleotides, resulting in RNA crimping. Despite reported functional differences, we observe few structural changes in ternary complexes with different ATP analogs. The structures constrain models of DEAD box protein function and reveal a strand separation mechanism in which a protein uses two wedges to act as a molecular crimper.

-	~~{{STRUCTURE_3i5y\| PDB=3i5y \| SCENE= }}~~	+	Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA.,Del Campo M, Lambowitz AM Mol Cell. 2009 Sep 11;35(5):598-609. PMID:19748356<ref>PMID:19748356</ref>

-	~~===Structure~~ of ~~Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19748356}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3i5y]] is a 2 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=3I5Y OCA].~~	+

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019748356<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Campo, M Del.]]		[[Category: Campo, M Del.]]

OCA at 20:41, 20 October 2012

OCA — Sat, 20 Oct 2012 20:41:32 GMT

←Older revision		Revision as of 20:41, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3i5y]] is a 2 chain structure ~~of [[Helicase]]~~ 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=3I5Y OCA].	+	[[3i5y]] is a 2 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=3I5Y OCA].

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

OCA: Protected "3i5y" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 11:18:49 GMT

Protected "3i5y" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:18, 27 July 2012

OCA at 11:18, 27 July 2012

OCA — Fri, 27 Jul 2012 11:18:48 GMT

←Older revision		Revision as of 11:18, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3i5y.png\|left\|200px]]		[[Image:3i5y.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i5y", 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_3i5y\| PDB=3i5y \| SCENE= }}		{{STRUCTURE_3i5y\| PDB=3i5y \| SCENE= }}

	===Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP===		===Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19748356}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19748356 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19748356}}		{{ABSTRACT_PUBMED_19748356}}

	==About this Structure==		==About this Structure==
-	~~3I5Y~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=3I5Y OCA].	+	[[3i5y]] is a 2 chain structure of [[Helicase]] 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=3I5Y OCA].
		+
		+	==See Also==
		+	*[[Helicase\|Helicase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19748356~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019748356</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Campo, M Del.]]		[[Category: Campo, M Del.]]
Line 31:		Line 22:
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Hydrolase/rna complex]]	+	[[Category: Hydrolase-rna complex]]
	[[Category: Mitochondrion]]		[[Category: Mitochondrion]]
	[[Category: Mrna processing]]		[[Category: Mrna processing]]
Line 41:		Line 32:
	[[Category: Transit peptide]]		[[Category: Transit peptide]]
	[[Category: Translation regulation]]		[[Category: Translation regulation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 30 08:52:54 2009''

OCA at 06:52, 30 September 2009

OCA — Wed, 30 Sep 2009 06:52:55 GMT

←Older revision		Revision as of 06:52, 30 September 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3i5y.~~jpg~~\|left\|200px]]	+	[[Image:3i5y.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP===		===Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19748356}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19748356 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19748356}}

	==About this Structure==		==About this Structure==
	3I5Y is a 2 chains structure of sequences 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=3I5Y OCA].		3I5Y is a 2 chains structure of sequences 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=3I5Y OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19748356</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Campo, M Del.]]		[[Category: Campo, M Del.]]
Line 33:		Line 42:
	[[Category: Translation regulation]]		[[Category: Translation regulation]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep ~~9 09~~:50:00 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 30 08:52:54 2009''