3pey - Revision history

OCA at 10:40, 21 February 2024

OCA — Wed, 21 Feb 2024 10:40:26 GMT

←Older revision		Revision as of 10:40, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3pey' size='340' side='right'caption='[[3pey]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3pey' size='340' side='right'caption='[[3pey]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pey]] 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=3PEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PEY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pey]] 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=3PEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PEY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.401Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DBP5, RAT8, YOR046C ([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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [https://pdbe.org/3pey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [https://www.ebi.ac.uk/pdbsum/3pey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pey 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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [https://pdbe.org/3pey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [https://www.ebi.ac.uk/pdbsum/3pey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pey ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DBP5_YEAST DBP5_YEAST]] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.<ref>PMID:9564047</ref> <ref>PMID:9564048</ref> <ref>PMID:10428971</ref> <ref>PMID:10610322</ref> <ref>PMID:10523319</ref> <ref>PMID:11350039</ref> <ref>PMID:12192043</ref> <ref>PMID:12686617</ref> <ref>PMID:15280434</ref> <ref>PMID:15574330</ref> <ref>PMID:15619606</ref>	+	[https://www.uniprot.org/uniprot/DBP5_YEAST DBP5_YEAST] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.<ref>PMID:9564047</ref> <ref>PMID:9564048</ref> <ref>PMID:10428971</ref> <ref>PMID:10610322</ref> <ref>PMID:10523319</ref> <ref>PMID:11350039</ref> <ref>PMID:12192043</ref> <ref>PMID:12686617</ref> <ref>PMID:15280434</ref> <ref>PMID:15574330</ref> <ref>PMID:15619606</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Superfamily 1 and superfamily 2 RNA helicases are ubiquitous messenger-RNA-protein complex (mRNP) remodelling enzymes that have critical roles in all aspects of RNA metabolism. The superfamily 2 DEAD-box ATPase Dbp5 (human DDX19) functions in mRNA export and is thought to remodel mRNPs at the nuclear pore complex (NPC). Dbp5 is localized to the NPC via an interaction with Nup159 (NUP214 in vertebrates) and is locally activated there by Gle1 together with the small-molecule inositol hexakisphosphate (InsP(6)). Local activation of Dbp5 at the NPC by Gle1 is essential for mRNA export in vivo; however, the mechanistic role of Dbp5 in mRNP export is poorly understood and it is not known how Gle1(InsP6) and Nup159 regulate the activity of Dbp5. Here we report, from yeast, structures of Dbp5 in complex with Gle1(InsP6), Nup159/Gle1(InsP6) and RNA. These structures reveal that InsP(6) functions as a small-molecule tether for the Gle1-Dbp5 interaction. Surprisingly, the Gle1(InsP6)-Dbp5 complex is structurally similar to another DEAD-box ATPase complex essential for translation initiation, eIF4G-eIF4A, and we demonstrate that Gle1(InsP6) and eIF4G both activate their DEAD-box partner by stimulating RNA release. Furthermore, Gle1(InsP6) relieves Dbp5 autoregulation and cooperates with Nup159 in stabilizing an open Dbp5 intermediate that precludes RNA binding. These findings explain how Gle1(InsP6), Nup159 and Dbp5 collaborate in mRNA export and provide a general mechanism for DEAD-box ATPase regulation by Gle1/eIF4G-like activators.	+
-		+
-	A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export.,Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K Nature. 2011 Apr 14;472(7342):238-42. Epub 2011 Mar 27. PMID:21441902<ref>PMID:21441902</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3pey" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RNA helicase~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Berger~~, J M~~]]	+	[[Category: Berger JM]]
-	[[Category: Helmke~~, K J~~]]	+	[[Category: Helmke KJ]]
-	[[Category: Montpetit, B]]	+	[[Category: Montpetit B]]
-	[[Category: Seeliger~~, M A~~]]	+	[[Category: Seeliger MA]]
-	[[Category: Thomsen~~, N D~~]]	+	[[Category: Thomsen ND]]
-	[[Category: Weis, K]]	+	[[Category: Weis K]]
-	~~[[Category: Atpase]]~~	+
-	~~[[Category: Dead-box]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Hydrolase-rna complex]]~~	+
-	~~[[Category: Mrna-export]]~~	+
-	~~[[Category: Nuclear pore]]~~	+
-	~~[[Category: Reca~~]]	+

OCA at 08:36, 25 May 2022

OCA — Wed, 25 May 2022 08:36:31 GMT

←Older revision		Revision as of 08:36, 25 May 2022
Line 1:		Line 1:

	==S. cerevisiae Dbp5 bound to RNA and ADP BeF3==		==S. cerevisiae Dbp5 bound to RNA and ADP BeF3==
-	<StructureSection load='3pey' size='340' side='right' caption='[[3pey]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='3pey' size='340' side='right'caption='[[3pey]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pey]] 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=3PEY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PEY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pey]] 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=3PEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PEY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DBP5, RAT8, YOR046C ([~~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">DBP5, RAT8, YOR046C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [~~http~~://pdbe.org/3pey PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pey PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pey 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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [https://pdbe.org/3pey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [https://www.ebi.ac.uk/pdbsum/3pey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pey ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DBP5_YEAST DBP5_YEAST]] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.<ref>PMID:9564047</ref> <ref>PMID:9564048</ref> <ref>PMID:10428971</ref> <ref>PMID:10610322</ref> <ref>PMID:10523319</ref> <ref>PMID:11350039</ref> <ref>PMID:12192043</ref> <ref>PMID:12686617</ref> <ref>PMID:15280434</ref> <ref>PMID:15574330</ref> <ref>PMID:15619606</ref>	+	[[https://www.uniprot.org/uniprot/DBP5_YEAST DBP5_YEAST]] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.<ref>PMID:9564047</ref> <ref>PMID:9564048</ref> <ref>PMID:10428971</ref> <ref>PMID:10610322</ref> <ref>PMID:10523319</ref> <ref>PMID:11350039</ref> <ref>PMID:12192043</ref> <ref>PMID:12686617</ref> <ref>PMID:15280434</ref> <ref>PMID:15574330</ref> <ref>PMID:15619606</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 3pey" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pey" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Berger, J M]]		[[Category: Berger, J M]]

OCA at 08:58, 8 November 2017

OCA — Wed, 08 Nov 2017 08:58:30 GMT

←Older revision		Revision as of 08:58, 8 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3pey" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pey" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Helicase\|Helicase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:42, 4 August 2016

OCA — Thu, 04 Aug 2016 14:42:19 GMT

←Older revision		Revision as of 14:42, 4 August 2016
Line 1:		Line 1:
		+
	==S. cerevisiae Dbp5 bound to RNA and ADP BeF3==		==S. cerevisiae Dbp5 bound to RNA and ADP BeF3==
	<StructureSection load='3pey' size='340' side='right' caption='[[3pey]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3pey' size='340' side='right' caption='[[3pey]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pey]] 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=3PEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PEY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pey]] 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=3PEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PEY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DBP5, RAT8, YOR046C ([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">DBP5, RAT8, YOR046C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [http://www.ebi.ac.uk/pdbsum/3pey 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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [http://pdbe.org/3pey PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [http://www.ebi.ac.uk/pdbsum/3pey PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pey ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3pey" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Berger, J M]]		[[Category: Berger, J M]]
	[[Category: Helmke, K J]]		[[Category: Helmke, K J]]

OCA at 15:55, 24 December 2014

OCA — Wed, 24 Dec 2014 15:55:28 GMT

←Older revision		Revision as of 15:55, 24 December 2014
Line 8:		Line 8:
	<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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [http://www.ebi.ac.uk/pdbsum/3pey 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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [http://www.ebi.ac.uk/pdbsum/3pey PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DBP5_YEAST DBP5_YEAST]] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.<ref>PMID:9564047</ref> <ref>PMID:9564048</ref> <ref>PMID:10428971</ref> <ref>PMID:10610322</ref> <ref>PMID:10523319</ref> <ref>PMID:11350039</ref> <ref>PMID:12192043</ref> <ref>PMID:12686617</ref> <ref>PMID:15280434</ref> <ref>PMID:15574330</ref> <ref>PMID:15619606</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:56, 9 December 2014

OCA — Tue, 09 Dec 2014 10:56:18 GMT

←Older revision		Revision as of 10:56, 9 December 2014
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-	[[~~Image:~~3pey.~~png~~\|~~left~~\|~~200px~~]]	+	==S. cerevisiae Dbp5 bound to RNA and ADP BeF3==
		+	<StructureSection load='3pey' size='340' side='right' caption='[[3pey]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3pey]] 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=3PEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PEY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DBP5, RAT8, YOR046C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=3pey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pey OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pey RCSB], [http://www.ebi.ac.uk/pdbsum/3pey PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Superfamily 1 and superfamily 2 RNA helicases are ubiquitous messenger-RNA-protein complex (mRNP) remodelling enzymes that have critical roles in all aspects of RNA metabolism. The superfamily 2 DEAD-box ATPase Dbp5 (human DDX19) functions in mRNA export and is thought to remodel mRNPs at the nuclear pore complex (NPC). Dbp5 is localized to the NPC via an interaction with Nup159 (NUP214 in vertebrates) and is locally activated there by Gle1 together with the small-molecule inositol hexakisphosphate (InsP(6)). Local activation of Dbp5 at the NPC by Gle1 is essential for mRNA export in vivo; however, the mechanistic role of Dbp5 in mRNP export is poorly understood and it is not known how Gle1(InsP6) and Nup159 regulate the activity of Dbp5. Here we report, from yeast, structures of Dbp5 in complex with Gle1(InsP6), Nup159/Gle1(InsP6) and RNA. These structures reveal that InsP(6) functions as a small-molecule tether for the Gle1-Dbp5 interaction. Surprisingly, the Gle1(InsP6)-Dbp5 complex is structurally similar to another DEAD-box ATPase complex essential for translation initiation, eIF4G-eIF4A, and we demonstrate that Gle1(InsP6) and eIF4G both activate their DEAD-box partner by stimulating RNA release. Furthermore, Gle1(InsP6) relieves Dbp5 autoregulation and cooperates with Nup159 in stabilizing an open Dbp5 intermediate that precludes RNA binding. These findings explain how Gle1(InsP6), Nup159 and Dbp5 collaborate in mRNA export and provide a general mechanism for DEAD-box ATPase regulation by Gle1/eIF4G-like activators.

-	~~{{STRUCTURE_3pey\| PDB=3pey \| SCENE= }}~~	+	A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export.,Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K Nature. 2011 Apr 14;472(7342):238-42. Epub 2011 Mar 27. PMID:21441902<ref>PMID:21441902</ref>

-	~~===S. cerevisiae Dbp5 bound to RNA and ADP BeF3===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21441902}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3pey]] 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=3PEY OCA].~~	+

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021441902<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Berger, J M.]]	+	[[Category: Berger, J M]]
-	[[Category: Helmke, K J.]]	+	[[Category: Helmke, K J]]
-	[[Category: Montpetit, B.]]	+	[[Category: Montpetit, B]]
-	[[Category: Seeliger, M A.]]	+	[[Category: Seeliger, M A]]
-	[[Category: Thomsen, N D.]]	+	[[Category: Thomsen, N D]]
-	[[Category: Weis, K.]]	+	[[Category: Weis, K]]
	[[Category: Atpase]]		[[Category: Atpase]]
	[[Category: Dead-box]]		[[Category: Dead-box]]

OCA at 06:55, 20 October 2012

OCA — Sat, 20 Oct 2012 06:55:14 GMT

←Older revision		Revision as of 06:55, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3pey]] 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=3PEY OCA].	+	[[3pey]] 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=3PEY OCA].

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

OCA at 14:44, 25 July 2012

OCA — Wed, 25 Jul 2012 14:44:43 GMT

←Older revision		Revision as of 14:44, 25 July 2012
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	[[Image:3pey.png\|left\|200px]]		[[Image:3pey.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3pey", 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_3pey\| PDB=3pey \| SCENE= }}		{{STRUCTURE_3pey\| PDB=3pey \| SCENE= }}

	===S. cerevisiae Dbp5 bound to RNA and ADP BeF3===		===S. cerevisiae Dbp5 bound to RNA and ADP BeF3===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21441902}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21441902 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21441902}}		{{ABSTRACT_PUBMED_21441902}}

	==About this Structure==		==About this Structure==
-	[[3pey]] 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=3PEY OCA].	+	[[3pey]] 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=3PEY OCA].
		+
		+	==See Also==
		+	*[[Helicase\|Helicase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21441902~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021441902</ref><references group="xtra"/>
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 31:		Line 23:
	[[Category: Thomsen, N D.]]		[[Category: Thomsen, N D.]]
	[[Category: Weis, K.]]		[[Category: Weis, K.]]
		+	[[Category: Atpase]]
		+	[[Category: Dead-box]]
		+	[[Category: Helicase]]
		+	[[Category: Hydrolase-rna complex]]
		+	[[Category: Mrna-export]]
		+	[[Category: Nuclear pore]]
		+	[[Category: Reca]]

OCA at 06:33, 27 April 2011

OCA — Wed, 27 Apr 2011 06:33:49 GMT

←Older revision		Revision as of 06:33, 27 April 2011
Line 1:		Line 1:
-	[[Image:3pey.~~jpg~~\|left\|200px]]	+	[[Image:3pey.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===S. cerevisiae Dbp5 bound to RNA and ADP BeF3===		===S. cerevisiae Dbp5 bound to RNA and ADP BeF3===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21441902}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21441902 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21441902}}

	==About this Structure==		==About this Structure==
	[[3pey]] 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=3PEY OCA].		[[3pey]] 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=3PEY OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21441902</ref><references group="xtra"/>
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 07:19, 23 March 2011

OCA — Wed, 23 Mar 2011 07:19:48 GMT

←Older revision		Revision as of 07:19, 23 March 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3pey.jpg\|left\|200px]]

-	The ~~entry 3pey~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3pey", 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_3pey\| PDB=3pey \| SCENE= }}

-	~~Authors: Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K~~.	+	===S. cerevisiae Dbp5 bound to RNA and ADP BeF3===

-	~~Description~~: S. cerevisiae ~~Dbp5 bound to~~ RNA ~~and ADP BeF3~~	+
		+	==About this Structure==
		+	[[3pey]] 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=3PEY OCA].
		+	[[Category: RNA helicase]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Berger, J M.]]
		+	[[Category: Helmke, K J.]]
		+	[[Category: Montpetit, B.]]
		+	[[Category: Seeliger, M A.]]
		+	[[Category: Thomsen, N D.]]
		+	[[Category: Weis, K.]]