6b4e - Revision history

OCA at 14:32, 4 October 2023

2023-10-04T14:32:30Z

← Older revision		Revision as of 14:32, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6b4e' size='340' side='right'caption='[[6b4e]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6b4e' size='340' side='right'caption='[[6b4e]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6B4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B4E FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=PRO:PROLINE'>PRO</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]] 1.75Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GLE1, BRR3, RSS1, YDL207W, D1049 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=559292 Baker~~'~~s yeast])~~, ~~NUP42, RIP1, UIP1, YDR192C, YD9346.04C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=559292 Baker~~'~~s yeast])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></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=6b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4e OCA], [~~http~~://pdbe.org/6b4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6b4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6b4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4e 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=6b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4e OCA], [https://pdbe.org/6b4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b4e RCSB], [https://www.ebi.ac.uk/pdbsum/6b4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/GLE1_YEAST GLE1_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10684247</ref> <ref>PMID:11336711</ref> <ref>PMID:15208322</ref> [[http://www.uniprot.org/uniprot/NUP42_YEAST NUP42_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP42 is specifically important for nuclear protein and mRNA export.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10805742</ref> <ref>PMID:10952996</ref> <ref>PMID:11387327</ref> <ref>PMID:12604785</ref> <ref>PMID:12917401</ref> <ref>PMID:15039779</ref>		[https://www.uniprot.org/uniprot/GLE1_YEAST GLE1_YEAST] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10684247</ref> <ref>PMID:11336711</ref> <ref>PMID:15208322</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Baker's yeast]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Cai, S W~~]]		[[Category: Saccharomyces cerevisiae S288C]]
	[[Category: ~~Correia, A R~~]]		[[Category: Cai SW]]
	[[Category: ~~Hoelz, A~~]]		[[Category: Correia AR]]
	[[Category: ~~Huber, F M]]~~		[[Category: Hoelz A]]
	~~[[Category: Jette, C~~ A]]		[[Category: Huber FM]]
	[[Category: ~~Lin, D H~~]]		[[Category: Jette CA]]
	[[Category: ~~Complex~~]]		[[Category: Lin DH]]
	[[Category: ~~Dead-box helicase]]~~
	~~[[Category: Mrna export]]~~
	~~[[Category: Nuclear pore complex]]~~
	~~[[Category: Transport protein~~]]

OCA at 17:09, 20 November 2019

2019-11-20T17:09:28Z

← Older revision		Revision as of 17:09, 20 November 2019
Line 1:		Line 1:

	==Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex==		==Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex==
	<StructureSection load='6b4e' size='340' side='right' caption='[[6b4e]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6b4e' size='340' side='right'caption='[[6b4e]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4E FirstGlance]. <br>
Line 21:		Line 21:

	==See Also==		==See Also==
	*[[Nucleoporin\|Nucleoporin]]		*[[Nucleoporin 3D structures\|Nucleoporin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
			[[Category: Large Structures]]
	[[Category: Cai, S W]]		[[Category: Cai, S W]]
	[[Category: Correia, A R]]		[[Category: Correia, A R]]

OCA at 07:46, 21 February 2019

2019-02-21T07:46:27Z

← Older revision		Revision as of 07:46, 21 February 2019
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6b4e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6b4e" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Nucleoporin\|Nucleoporin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:51, 27 June 2018

2018-06-27T05:51:45Z

← Older revision		Revision as of 05:51, 27 June 2018
Line 3:		Line 3:
	<StructureSection load='6b4e' size='340' side='right' caption='[[6b4e]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6b4e' size='340' side='right' caption='[[6b4e]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLE1, BRR3, RSS1, YDL207W, D1049 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), NUP42, RIP1, UIP1, YDR192C, YD9346.04C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=6b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4e OCA], [http://pdbe.org/6b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b4e RCSB], [http://www.ebi.ac.uk/pdbsum/6b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4e ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4e OCA], [http://pdbe.org/6b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b4e RCSB], [http://www.ebi.ac.uk/pdbsum/6b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GLE1_YEAST GLE1_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10684247</ref> <ref>PMID:11336711</ref> <ref>PMID:15208322</ref> [[http://www.uniprot.org/uniprot/NUP42_YEAST NUP42_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP42 is specifically important for nuclear protein and mRNA export.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10805742</ref> <ref>PMID:10952996</ref> <ref>PMID:11387327</ref> <ref>PMID:12604785</ref> <ref>PMID:12917401</ref> <ref>PMID:15039779</ref>		[[http://www.uniprot.org/uniprot/GLE1_YEAST GLE1_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10684247</ref> <ref>PMID:11336711</ref> <ref>PMID:15208322</ref> [[http://www.uniprot.org/uniprot/NUP42_YEAST NUP42_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP42 is specifically important for nuclear protein and mRNA export.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10805742</ref> <ref>PMID:10952996</ref> <ref>PMID:11387327</ref> <ref>PMID:12604785</ref> <ref>PMID:12917401</ref> <ref>PMID:15039779</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1Nxt1 from mRNAs. Here, we report crystal structures of Gle1Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP6, unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor neuron diseases cause decreased Gle1 thermostability, implicating nucleoporin misfolding as a disease determinant. Crystal structures of human Gle1Nup42DDX19 reveal the structural rearrangements in DDX19 from an auto-inhibited to an RNA-binding competent state. Together, our results provide the foundation for further mechanistic analyses of mRNA export in humans.

			Structural and functional analysis of mRNA export regulation by the nuclear pore complex.,Lin DH, Correia AR, Cai SW, Huber FM, Jette CA, Hoelz A Nat Commun. 2018 Jun 13;9(1):2319. doi: 10.1038/s41467-018-04459-3. PMID:29899397<ref>PMID:29899397</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6b4e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Baker's yeast]]
	[[Category: Cai, S W]]		[[Category: Cai, S W]]
	[[Category: Correia, A R]]		[[Category: Correia, A R]]

OCA at 05:47, 20 June 2018

2018-06-20T05:47:13Z

@@ Line 1: / Line 1: @@
-The entry 6b4e is ON HOLD  until Paper Publication
+==Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex==
+<StructureSection load='6b4e' size='340' side='right' caption='[[6b4e]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4E FirstGlance]. <br>
-Description:
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>
-[[Category: Unreleased Structures]]
+<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=6b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4e OCA], [http://pdbe.org/6b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b4e RCSB], [http://www.ebi.ac.uk/pdbsum/6b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4e ProSAT]</span></td></tr>

OCA at 04:51, 1 November 2017

2017-11-01T04:51:10Z

← Older revision		Revision as of 04:51, 1 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6b4e is ON HOLD		The entry 6b4e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6b4e" [edit=sysop:move=sysop]

2017-10-04T08:13:25Z

Protected "6b4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:13, 4 October 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6b4e is ON HOLD Authors: Description: Category: Unreleased Structures

2017-10-04T08:13:24Z

New page: '''Unreleased structure''' The entry 6b4e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6b4e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]