2db3 - Revision history

OCA at 13:47, 13 March 2024

2024-03-13T13:47:08Z

← Older revision		Revision as of 13:47, 13 March 2024
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	<StructureSection load='2db3' size='340' side='right'caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2db3' size='340' side='right'caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DB3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DB3 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]] 2.2Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>VASA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~7227 DROME])</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~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3]~~ </~~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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [https://pdbe.org/2db3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [https://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2db3 ProSAT], [https://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [https://pdbe.org/2db3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [https://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2db3 ProSAT], [https://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/VASA1_DROME VASA1_DROME]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles during germ cell formation. Required for gus, Fsn and aub accumulation at the posterior pole of the embryo. Required for the localization of vas to the perinuclear region of nurse cells.<ref>PMID:10678180</ref> <ref>PMID:11526087</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref> <ref>PMID:18590813</ref> <ref>PMID:20123973</ref> <ref>PMID:3052853</ref> <ref>PMID:3140040</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</ref>		[https://www.uniprot.org/uniprot/VASA1_DROME VASA1_DROME] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles during germ cell formation. Required for gus, Fsn and aub accumulation at the posterior pole of the embryo. Required for the localization of vas to the perinuclear region of nurse cells.<ref>PMID:10678180</ref> <ref>PMID:11526087</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref> <ref>PMID:18590813</ref> <ref>PMID:20123973</ref> <ref>PMID:3052853</ref> <ref>PMID:3140040</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</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=2db3 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=2db3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein Vasa in complex with a single-stranded RNA and an ATP analog. The ATP analog intensively interacts with both of the domains, thereby bringing them into the closed form, with many interdomain interactions of conserved residues. The bound RNA is sharply bent, avoiding a clash with a conserved alpha helix in the N-terminal domain. This "wedge" helix should disrupt base pairs by bending one of the strands when a duplex is bound. Mutational analyses indicated that the interdomain interactions couple ATP hydrolysis to RNA unwinding, probably through fine positioning of the duplex relative to the wedge helix. This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures.

	Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.,Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S Cell. 2006 Apr 21;125(2):287-300. PMID:16630817<ref>PMID:16630817</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2db3" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Adenosinetriphosphatase]]~~		[[Category: Drosophila melanogaster]]
	~~[[Category: Drome~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kobayashi, S]]		[[Category: Kobayashi S]]
	[[Category: Nakamura, A]]		[[Category: Nakamura A]]
	[[Category: Nureki, O]]		[[Category: Nureki O]]
	~~[[Category: Structural genomic~~]]		[[Category: Sengoku T]]
	[[Category: Sengoku, T]]		[[Category: Yokoyama S]]
	[[Category: Yokoyama, S]]
	~~[[Category: Atpase]]~~
	~~[[Category: Dead-box]]~~
	~~[[Category: Helicase]]~~
	~~[[Category: Hydrolase-rna complex]]~~
	~~[[Category: Protein-rna complex]]~~
	~~[[Category: Rsgi~~]]

OCA at 11:59, 3 February 2021

2021-02-03T11:59:10Z

← Older revision		Revision as of 11:59, 3 February 2021
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	==Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa==		==Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa==
	<StructureSection load='2db3' size='340' side='right' caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2db3' size='340' side='right'caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DB3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DB3 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [~~http~~://pdbe.org/2db3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2db3 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [https://pdbe.org/2db3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [https://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2db3 ProSAT], [https://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/VASA1_DROME VASA1_DROME]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles during germ cell formation. Required for gus, Fsn and aub accumulation at the posterior pole of the embryo. Required for the localization of vas to the perinuclear region of nurse cells.<ref>PMID:10678180</ref> <ref>PMID:11526087</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref> <ref>PMID:18590813</ref> <ref>PMID:20123973</ref> <ref>PMID:3052853</ref> <ref>PMID:3140040</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</ref>		[[https://www.uniprot.org/uniprot/VASA1_DROME VASA1_DROME]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles during germ cell formation. Required for gus, Fsn and aub accumulation at the posterior pole of the embryo. Required for the localization of vas to the perinuclear region of nurse cells.<ref>PMID:10678180</ref> <ref>PMID:11526087</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref> <ref>PMID:18590813</ref> <ref>PMID:20123973</ref> <ref>PMID:3052853</ref> <ref>PMID:3140040</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Adenosinetriphosphatase]]		[[Category: Adenosinetriphosphatase]]
	[[Category: Drome]]		[[Category: Drome]]
			[[Category: Large Structures]]
	[[Category: Kobayashi, S]]		[[Category: Kobayashi, S]]
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]

OCA at 06:41, 30 May 2018

2018-05-30T06:41:30Z

← Older revision		Revision as of 06:41, 30 May 2018
Line 1:		Line 1:

	==Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa==		==Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa==
	<StructureSection load='2db3' size='340' side='right' caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2db3' size='340' side='right' caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://pdbe.org/2db3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://pdbe.org/2db3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2db3 ProSAT], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/db/2db3_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/2db3_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>
	</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=2db3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:53, 11 September 2015

2015-09-11T10:53:53Z

← Older revision		Revision as of 10:53, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2db3' size='340' side='right' caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2db3' size='340' side='right' caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Drosophila_melanogaster Drosophila melanogaster~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DB3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DB3 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 ~~Drosophila melanogaster~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://pdbe.org/2db3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~VASA_DROME VASA_DROME~~]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles.<ref>PMID:~~3140040~~</ref> <ref>PMID:~~3052853~~</ref> <ref>PMID:~~8026330~~</ref> <ref>PMID:~~9521895~~</ref> <ref>PMID:~~10678180~~</ref> <ref>PMID:~~12479811~~</ref> <ref>PMID:~~14588248~~</ref> <ref>PMID:~~16630817~~</ref>		[[http://www.uniprot.org/uniprot/VASA1_DROME VASA1_DROME]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles during germ cell formation. Required for gus, Fsn and aub accumulation at the posterior pole of the embryo. Required for the localization of vas to the perinuclear region of nurse cells.<ref>PMID:10678180</ref> <ref>PMID:11526087</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref> <ref>PMID:18590813</ref> <ref>PMID:20123973</ref> <ref>PMID:3052853</ref> <ref>PMID:3140040</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		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 2db3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Adenosinetriphosphatase]]		[[Category: Adenosinetriphosphatase]]
	[[Category: ~~Drosophila melanogaster~~]]		[[Category: Drome]]
	[[Category: Kobayashi, S]]		[[Category: Kobayashi, S]]
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]

OCA at 15:29, 25 December 2014

2014-12-25T15:29:17Z

← Older revision		Revision as of 15:29, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DB3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DB3 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>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </span></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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/VASA_DROME VASA_DROME]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles.<ref>PMID:3140040</ref> <ref>PMID:3052853</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</ref> <ref>PMID:10678180</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Adenosinetriphosphatase]]		[[Category: Adenosinetriphosphatase]]
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]
	[[Category: Kobayashi, S.]]		[[Category: Kobayashi, S]]
	[[Category: Nakamura, A.]]		[[Category: Nakamura, A]]
	[[Category: Nureki, O.]]		[[Category: Nureki, O]]
	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]		[[Category: Structural genomic]]
	[[Category: Sengoku, T.]]		[[Category: Sengoku, T]]
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S]]
	[[Category: Atpase]]		[[Category: Atpase]]
	[[Category: Dead-box]]		[[Category: Dead-box]]
Line 46:		Line 48:
	[[Category: Hydrolase-rna complex]]		[[Category: Hydrolase-rna complex]]
	[[Category: Protein-rna complex]]		[[Category: Protein-rna complex]]
	~~[[Category: Riken structural genomics/proteomics initiative]]~~
	[[Category: Rsgi]]		[[Category: Rsgi]]
	~~[[Category: Structural genomic]]~~

OCA at 02:32, 29 September 2014

2014-09-29T02:32:07Z

← Older revision		Revision as of 02:32, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2db3~~.~~png~~\|~~left~~\|~~200px~~]]		==Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa==
			<StructureSection load='2db3' size='340' side='right' caption='[[2db3]], [[Resolution\|resolution]] 2.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DB3 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>[[Gene\|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </span></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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</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/db/2db3_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 ==
			DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein Vasa in complex with a single-stranded RNA and an ATP analog. The ATP analog intensively interacts with both of the domains, thereby bringing them into the closed form, with many interdomain interactions of conserved residues. The bound RNA is sharply bent, avoiding a clash with a conserved alpha helix in the N-terminal domain. This "wedge" helix should disrupt base pairs by bending one of the strands when a duplex is bound. Mutational analyses indicated that the interdomain interactions couple ATP hydrolysis to RNA unwinding, probably through fine positioning of the duplex relative to the wedge helix. This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures.

	~~{{STRUCTURE_2db3\| PDB=2db3 \| SCENE= }}~~		Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.,Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S Cell. 2006 Apr 21;125(2):287-300. PMID:16630817<ref>PMID:16630817</ref>

	~~===Structural basis for RNA unwinding by~~ the ~~DEAD-box protein Drosophila Vasa===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16630817}}~~

	~~==About this Structure==~~
	~~[[2db3]] is a 8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Drosophila_melanogaster Drosophila melanogaster]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2DB3 OCA].~~

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016630817<~~/~~ref~~><~~ref group="xtra">PMID:014747711</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Adenosinetriphosphatase]]		[[Category: Adenosinetriphosphatase]]
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]

OCA at 18:20, 20 October 2012

2012-10-20T18:20:23Z

← Older revision		Revision as of 18:20, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2db3]] is a 8 chain structure ~~of [[Helicase]]~~ with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA].		[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA].

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

OCA at 03:47, 27 July 2012

2012-07-27T03:47:55Z

← Older revision		Revision as of 03:47, 27 July 2012
Line 1:		Line 1:
	[[Image:2db3.png\|left\|200px]]		[[Image:2db3.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2db3", 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_2db3\| PDB=2db3 \| SCENE= }}		{{STRUCTURE_2db3\| PDB=2db3 \| SCENE= }}

	===Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa===		===Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16630817}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16630817 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16630817}}		{{ABSTRACT_PUBMED_16630817}}

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	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
	*[[User:Wayne Decatur\|User:Wayne Decatur]]

	==Reference==		==Reference==

OCA: Protected "2db3" [edit=sysop:move=sysop]

2012-06-06T13:43:48Z

Protected "2db3" [edit=sysop:move=sysop]

← Older revision	Revision as of 13:43, 6 June 2012
(No difference)