1xtj - Revision history

OCA at 06:49, 23 August 2023

2023-08-23T06:49:18Z

←Older revision		Revision as of 06:49, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1xtj' size='340' side='right'caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1xtj' size='340' side='right'caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xtj]] is a 1 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=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xtj]] is a 1 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=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1xti\|1xti]], [[1xtk\|1xtk]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [https://pdbe.org/1xtj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [https://www.ebi.ac.uk/pdbsum/1xtj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xtj ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [~~http~~://pdbe.org/1xtj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xtj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xtj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DX39B_HUMAN DX39B_HUMAN]] Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. The recruitment of the TREX complex to the intronless viral mRNA occurs via an interaction between KSHV ORF57 protein and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref> Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref>	+	[https://www.uniprot.org/uniprot/DX39B_HUMAN DX39B_HUMAN] Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. The recruitment of the TREX complex to the intronless viral mRNA occurs via an interaction between KSHV ORF57 protein and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref> Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cordin, O]]	+	[[Category: Cordin O]]
-	[[Category: Linder, P]]	+	[[Category: Linder P]]
-	[[Category: Minder~~, C M~~]]	+	[[Category: Minder CM]]
-	[[Category: Shi, H]]	+	[[Category: Shi H]]
-	[[Category: Xu, R M]]	+	[[Category: Xu R-M]]
-	~~[[Category: Alpha-beta fold]]~~	+
-	~~[[Category: Gene regulation~~]]	+

OCA at 10:19, 6 January 2021

2021-01-06T10:19:45Z

←Older revision		Revision as of 10:19, 6 January 2021
Line 1:		Line 1:

	==structure of human UAP56 in complex with ADP==		==structure of human UAP56 in complex with ADP==
-	<StructureSection load='1xtj' size='340' side='right' caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1xtj' size='340' side='right'caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xtj]] is a 1 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=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xtj]] is a 1 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=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xti\|1xti]], [[1xtk\|1xtk]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://pdbe.org/1xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xtj ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://pdbe.org/1xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xtj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cordin, O]]		[[Category: Cordin, O]]
	[[Category: Linder, P]]		[[Category: Linder, P]]

OCA at 07:39, 18 April 2018

2018-04-18T07:39:59Z

←Older revision		Revision as of 07:39, 18 April 2018
Line 1:		Line 1:
		+
	==structure of human UAP56 in complex with ADP==		==structure of human UAP56 in complex with ADP==
	<StructureSection load='1xtj' size='340' side='right' caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1xtj' size='340' side='right' caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://pdbe.org/1xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj 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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://pdbe.org/1xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xtj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xt/1xtj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xt/1xtj_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 21:05, 8 February 2016

2016-02-08T21:05:01Z

←Older revision		Revision as of 21:05, 8 February 2016
Line 18:		Line 18:
	<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=1xtj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:22, 10 September 2015

2015-09-10T15:22:46Z

←Older revision		Revision as of 15:22, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1xtj' size='340' side='right' caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1xtj' size='340' side='right' caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xtj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xtj]] is a 1 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=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj 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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://pdbe.org/1xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~UAP56_HUMAN UAP56_HUMAN~~]] Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. The recruitment of the TREX complex to the intronless viral mRNA occurs via an interaction between KSHV ORF57 protein and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref> Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref>	+	[[http://www.uniprot.org/uniprot/DX39B_HUMAN DX39B_HUMAN]] Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. The recruitment of the TREX complex to the intronless viral mRNA occurs via an interaction between KSHV ORF57 protein and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref> Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</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 1xtj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cordin, O]]		[[Category: Cordin, O]]
	[[Category: Linder, P]]		[[Category: Linder, P]]

OCA at 02:08, 25 December 2014

2014-12-25T02:08:10Z

←Older revision		Revision as of 02:08, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xtj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xtj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj 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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UAP56_HUMAN UAP56_HUMAN]] Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. The recruitment of the TREX complex to the intronless viral mRNA occurs via an interaction between KSHV ORF57 protein and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref> Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.<ref>PMID:9242493</ref> <ref>PMID:11675789</ref> <ref>PMID:15833825</ref> <ref>PMID:15998806</ref> <ref>PMID:17190602</ref> <ref>PMID:17562711</ref> <ref>PMID:18974867</ref> <ref>PMID:15585580</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cordin, O.]]	+	[[Category: Cordin, O]]
-	[[Category: Linder, P.]]	+	[[Category: Linder, P]]
-	[[Category: Minder, C M.]]	+	[[Category: Minder, C M]]
-	[[Category: Shi, H.]]	+	[[Category: Shi, H]]
-	[[Category: Xu, R M.]]	+	[[Category: Xu, R M]]
	[[Category: Alpha-beta fold]]		[[Category: Alpha-beta fold]]
	[[Category: Gene regulation]]		[[Category: Gene regulation]]

OCA at 21:41, 29 September 2014

2014-09-29T21:41:51Z

←Older revision		Revision as of 21:41, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xtj.~~png~~\|~~left~~\|200px]]	+	==structure of human UAP56 in complex with ADP==
		+	<StructureSection load='1xtj' size='340' side='right' caption='[[1xtj]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xtj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XTJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xti\|1xti]], [[1xtk\|1xtk]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=1xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xtj RCSB], [http://www.ebi.ac.uk/pdbsum/1xtj PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xt/1xtj_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 ==
		+	Pre-mRNA splicing requires the function of a number of RNA-dependent ATPases/helicases, yet no three-dimensional structure of any spliceosomal ATPases/helicases is known. The highly conserved DECD-box protein UAP56/Sub2 is an essential splicing factor that is also important for mRNA export. The expected ATPase/helicase activity appears to be essential for the UAP56/Sub2 functions. Here, we show that purified human UAP56 is an active RNA-dependent ATPase, and we also report the crystal structures of UAP56 alone and in complex with ADP, as well as a DECD to DEAD mutant. The structures reveal a unique spatial arrangement of the two conserved helicase domains, and ADP-binding induces significant conformational changes of key residues in the ATP-binding pocket. Our structural analyses suggest a specific protein-RNA displacement model of UAP56/Sub2. The detailed structural information provides important mechanistic insights into the splicing function of UAP56/Sub2. The structures also will be useful for the analysis of other spliceosomal DExD-box ATPases/helicases.

-	~~{{STRUCTURE_1xtj\| PDB=1xtj \| SCENE= }}~~	+	Crystal structure of the human ATP-dependent splicing and export factor UAP56.,Shi H, Cordin O, Minder CM, Linder P, Xu RM Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17628-33. Epub 2004 Dec 7. PMID:15585580<ref>PMID:15585580</ref>

-	~~===structure~~ of ~~human UAP56 in complex with ADP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15585580}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xtj]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XTJ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015585580<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cordin, O.]]		[[Category: Cordin, O.]]

OCA: Protected "1xtj" [edit=sysop:move=sysop]

2013-01-05T13:06:14Z

Protected "1xtj" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:06, 5 January 2013

OCA at 13:06, 5 January 2013

2013-01-05T13:06:11Z

←Older revision		Revision as of 13:06, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xtj.png\|left\|200px]]		[[Image:1xtj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xtj", 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_1xtj\| PDB=1xtj \| SCENE= }}		{{STRUCTURE_1xtj\| PDB=1xtj \| SCENE= }}

	===structure of human UAP56 in complex with ADP===		===structure of human UAP56 in complex with ADP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15585580}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15585580 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15585580}}		{{ABSTRACT_PUBMED_15585580}}

	==About this Structure==		==About this Structure==
-	~~1XTJ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTJ OCA].	+	[[1xtj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTJ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15585580~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015585580</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cordin, O.]]		[[Category: Cordin, O.]]
Line 32:		Line 20:
	[[Category: Alpha-beta fold]]		[[Category: Alpha-beta fold]]
	[[Category: Gene regulation]]		[[Category: Gene regulation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 22 10:58:44 2009''

OCA at 07:58, 22 April 2009

2009-04-22T07:58:45Z

←Older revision		Revision as of 07:58, 22 April 2009
Line 31:		Line 31:
	[[Category: Xu, R M.]]		[[Category: Xu, R M.]]
	[[Category: Alpha-beta fold]]		[[Category: Alpha-beta fold]]
		+	[[Category: Gene regulation]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 03~~:20:19 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 22 10:58:44 2009''