6b4i - Revision history

OCA at 14:20, 13 March 2024

OCA — Wed, 13 Mar 2024 14:20:16 GMT

←Older revision		Revision as of 14:20, 13 March 2024
Line 1:		Line 1:

	==Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex==		==Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex==
-	<StructureSection load='6b4i' size='340' side='right' caption='[[6b4i]], [[Resolution\|resolution]] 3.62Å' scene=''>	+	<StructureSection load='6b4i' size='340' side='right'caption='[[6b4i]], [[Resolution\|resolution]] 3.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b4i]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6B4I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b4i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B4I 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=PO4:PHOSPHATE+ION'>PO4</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]] 3.619Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>GLE1, GLE1L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), NUPL2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), DDX19B, DBP5, DDX19, TDBP ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=9606 HUMAN])</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=PO4:PHOSPHATE+ION'>PO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6b4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4i OCA], [https://pdbe.org/6b4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b4i RCSB], [https://www.ebi.ac.uk/pdbsum/6b4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4i 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=6b4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4i OCA], [~~http~~://pdbe.org/6b4i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6b4i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6b4i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN]] Lethal arthrogryposis - anterior horn cell disease;Lethal congenital contracture syndrome type 1. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN] Lethal arthrogryposis - anterior horn cell disease;Lethal congenital contracture syndrome type 1. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN]] Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm. May be involved in the terminal step of the mRNA transport through the nuclear pore complex (NPC).<ref>PMID:12668658</ref> <ref>PMID:16000379</ref> <ref>PMID:9618489</ref> [[http://www.uniprot.org/uniprot/DD19B_HUMAN DD19B_HUMAN]] ATP-dependent RNA helicase involved in mRNA export from the nucleus. Rather than unwinding RNA duplexes, DDX19B functions as a remodeler of ribonucleoprotein particles, whereby proteins bound to nuclear mRNA are dissociated and replaced by cytoplasmic mRNA binding proteins.	+	[https://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN] Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm. May be involved in the terminal step of the mRNA transport through the nuclear pore complex (NPC).<ref>PMID:12668658</ref> <ref>PMID:16000379</ref> <ref>PMID:9618489</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>	+	==See Also==
-		+	*[[Helicase 3D structures\|Helicase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6b4i" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~RNA helicase~~]]	+	[[Category: Large Structures]]
-	[[Category: Cai~~, S W~~]]	+	[[Category: Cai SW]]
-	[[Category: Correia~~, A R~~]]	+	[[Category: Correia AR]]
-	[[Category: Hoelz, A]]	+	[[Category: Hoelz A]]
-	[[Category: Huber~~, F M~~]]	+	[[Category: Huber FM]]
-	[[Category: Jette~~, C A~~]]	+	[[Category: Jette CA]]
-	[[Category: Lin~~, D H]]~~	+	[[Category: Lin DH]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dead-box helicase]]~~	+
-	~~[[Category: Mrna export]]~~	+
-	~~[[Category: Nuclear pore complex]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 05:52, 27 June 2018

OCA — Wed, 27 Jun 2018 05:52:17 GMT

←Older revision		Revision as of 05:52, 27 June 2018
Line 3:		Line 3:
	<StructureSection load='6b4i' size='340' side='right' caption='[[6b4i]], [[Resolution\|resolution]] 3.62Å' scene=''>		<StructureSection load='6b4i' size='340' side='right' caption='[[6b4i]], [[Resolution\|resolution]] 3.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b4i]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b4i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4I 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=PO4:PHOSPHATE+ION'>PO4</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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLE1, GLE1L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NUPL2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DDX19B, DBP5, DDX19, TDBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6b4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4i OCA], [http://pdbe.org/6b4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b4i RCSB], [http://www.ebi.ac.uk/pdbsum/6b4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4i 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=6b4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4i OCA], [http://pdbe.org/6b4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b4i RCSB], [http://www.ebi.ac.uk/pdbsum/6b4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4i ProSAT]</span></td></tr>
Line 12:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN]] Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm. May be involved in the terminal step of the mRNA transport through the nuclear pore complex (NPC).<ref>PMID:12668658</ref> <ref>PMID:16000379</ref> <ref>PMID:9618489</ref> [[http://www.uniprot.org/uniprot/DD19B_HUMAN DD19B_HUMAN]] ATP-dependent RNA helicase involved in mRNA export from the nucleus. Rather than unwinding RNA duplexes, DDX19B functions as a remodeler of ribonucleoprotein particles, whereby proteins bound to nuclear mRNA are dissociated and replaced by cytoplasmic mRNA binding proteins.		[[http://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN]] Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm. May be involved in the terminal step of the mRNA transport through the nuclear pore complex (NPC).<ref>PMID:12668658</ref> <ref>PMID:16000379</ref> <ref>PMID:9618489</ref> [[http://www.uniprot.org/uniprot/DD19B_HUMAN DD19B_HUMAN]] ATP-dependent RNA helicase involved in mRNA export from the nucleus. Rather than unwinding RNA duplexes, DDX19B functions as a remodeler of ribonucleoprotein particles, whereby proteins bound to nuclear mRNA are dissociated and replaced by cytoplasmic mRNA binding proteins.
		+	<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 6b4i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Cai, S W]]		[[Category: Cai, S W]]

OCA at 05:47, 20 June 2018

OCA — Wed, 20 Jun 2018 05:47:51 GMT

←Older revision		Revision as of 05:47, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~6b4i~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex==
-		+	<StructureSection load='6b4i' size='340' side='right' caption='[[6b4i]], [[Resolution\|resolution]] 3.62Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6b4i]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4I FirstGlance]. <br>
-	~~Description~~:	+	</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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6b4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4i OCA], [http://pdbe.org/6b4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b4i RCSB], [http://www.ebi.ac.uk/pdbsum/6b4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4i ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN]] Lethal arthrogryposis - anterior horn cell disease;Lethal congenital contracture syndrome type 1. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLE1_HUMAN GLE1_HUMAN]] Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm. May be involved in the terminal step of the mRNA transport through the nuclear pore complex (NPC).<ref>PMID:12668658</ref> <ref>PMID:16000379</ref> <ref>PMID:9618489</ref> [[http://www.uniprot.org/uniprot/DD19B_HUMAN DD19B_HUMAN]] ATP-dependent RNA helicase involved in mRNA export from the nucleus. Rather than unwinding RNA duplexes, DDX19B functions as a remodeler of ribonucleoprotein particles, whereby proteins bound to nuclear mRNA are dissociated and replaced by cytoplasmic mRNA binding proteins.
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RNA helicase]]
		+	[[Category: Cai, S W]]
		+	[[Category: Correia, A R]]
		+	[[Category: Hoelz, A]]
		+	[[Category: Huber, F M]]
		+	[[Category: Jette, C A]]
		+	[[Category: Lin, D H]]
		+	[[Category: Complex]]
		+	[[Category: Dead-box helicase]]
		+	[[Category: Mrna export]]
		+	[[Category: Nuclear pore complex]]
		+	[[Category: Transport protein]]

OCA at 04:51, 1 November 2017

OCA — Wed, 01 Nov 2017 04:51:21 GMT

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

-	The entry 6b4i is ON HOLD	+	The entry 6b4i is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6b4i" [edit=sysop:move=sysop]

OCA — Wed, 04 Oct 2017 08:13:37 GMT

Protected "6b4i" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:13, 4 October 2017

OCA: New page: '''Unreleased structure''' The entry 6b4i is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Oct 2017 08:13:35 GMT

New page: '''Unreleased structure''' The entry 6b4i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6b4i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]