4px9 - Revision history

OCA at 17:24, 20 September 2023

OCA — Wed, 20 Sep 2023 17:24:12 GMT

←Older revision		Revision as of 17:24, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4px9]] is a 3 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=4PX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PX9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4px9]] is a 3 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=4PX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PX9 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></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]] 2.31Å</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></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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [https://pdbe.org/4px9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [https://www.ebi.ac.uk/pdbsum/4px9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4px9 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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [https://pdbe.org/4px9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [https://www.ebi.ac.uk/pdbsum/4px9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4px9 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:36, 8 February 2023

OCA — Wed, 08 Feb 2023 07:36:06 GMT

←Older revision		Revision as of 07:36, 8 February 2023
Line 1:		Line 1:

	==DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop==		==DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop==
-	<StructureSection load='4px9' size='340' side='right' caption='[[4px9]], [[Resolution\|resolution]] 2.31Å' scene=''>	+	<StructureSection load='4px9' size='340' side='right'caption='[[4px9]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4px9]] is a 3 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=4PX9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4px9]] is a 3 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=4PX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PX9 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~~></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></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxa\|4pxa]]</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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [https://pdbe.org/4px9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [https://www.ebi.ac.uk/pdbsum/4px9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4px9 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DBX, DDX3, DDX3X ([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='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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [~~http~~://pdbe.org/4px9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4px9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4px9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DDX3X_HUMAN DDX3X_HUMAN]] Multifunctional ATP-dependent RNA helicase. The ATPase activity can be stimulated by various ribo- and deoxynucleic acids indicative for a relaxed substrate specificity. In vitro can unwind partially double stranded DNA with a preference for 5'-single stranded DNA overhangs. Is involved in several steps of gene expression, such as transcription, mRNA maturation, mRNA export and translation. However, the exact mechanisms are not known and some functions may be specific for a subset of mRNAs. Involved in transcriptional regulation. Can enhance transcription from the CDKN1A/WAF1 promoter in a SP1-dependent manner. Found associated with the E-cadherin promoter and can down-regulate transcription from the promoter. Involved in regulation of translation initiation. Proposed to be involved in positive regulation of translation such as of cyclin E1/CCNE1 mRNA and specifically of mRNAs containing complex secondary structures in their 5'UTRs; these functions seem to require RNA helicase activity. Specifically promotes translation of a subset of viral and cellular mRNAs carrying a 5'proximal stem-loop structure in their 5'UTRs and cooperates with the eIF4F complex. Proposed to act prior to 43S ribosomal scanning and to locally destabilize these RNA structures to allow recognition of the mRNA cap or loading onto the 40S subunit. After association with 40S ribosomal subunits seems to be involved in the functional assembly of 80S ribosomes; the function seems to cover translation of mRNAs with structured and non-structured 5'UTRs and is independent of RNA helicase activity. Also proposed to inhibit cap-dependent translation by competetive interaction with EIF4E which can block the EIF4E:EIF4G complex formation. Proposed to be involved in stress response and stress granule assembly; the function is independent of RNA helicase activity and seems to involve association with EIF4E. May be involved in nuclear export of specific mRNAs but not in bulk mRNA export via interactions with XPO1 and NXF1. Also associates with polyadenylated mRNAs independently of NXF1. Associates with spliced mRNAs in an exon junction complex (EJC)-dependent manner and seems not to be directly involved in splicing. May be involved in nuclear mRNA export by association with DDX5 and regulating its nuclear location. Involved in innate immune signaling promoting the production of type I interferon (IFN-alpha and IFN-beta); proposed to act as viral RNA sensor, signaling intermediate and transcriptional coactivator. Involved in TBK1 and IKBKE-dependent IRF3 activation leading to IFN-beta induction. Also found associated with IFN-beta promoters; the function is independent of IRF3. Can bind to viral RNAs and via association with MAVS/IPS1 and DDX58/RIG-I is thought to induce signaling in early stages of infection. Involved in regulation of apoptosis. May be required for activation of the intrinsic but inhibit activation of the extrinsic apoptotic pathway. Acts as an antiapoptotic protein through association with GSK3A/B and BIRC2 in an apoptosis antagonizing signaling complex; activation of death receptors promotes caspase-dependent cleavage of BIRC2 and DDX3X and relieves the inhibition. May be involved in mitotic chromosome segregation. Appears to be a prime target for viral manipulations. Hepatitis B virus (HBV) polymerase and possibly vaccinia virus (VACV) protein K7 inhibit IFN-beta induction probably by dissociating DDX3X from TBK1 or IKBKE. Is involved in hepatitis C virus (HCV) replication; the function may involve the association with HCV core protein. HCV core protein inhibits the IPS1-dependent function in viral RNA sensing and may switch the function from a INF-beta inducing to a HCV replication mode. Involved in HIV-1 replication. Acts as a cofactor for XPO1-mediated nuclear export of incompletely spliced HIV-1 Rev RNAs.<ref>PMID:10329544</ref> <ref>PMID:15507209</ref> <ref>PMID:16818630</ref> <ref>PMID:16301996</ref> <ref>PMID:17357160</ref> <ref>PMID:18846110</ref> <ref>PMID:18583960</ref> <ref>PMID:18636090</ref> <ref>PMID:18596238</ref> <ref>PMID:18628297</ref> <ref>PMID:17667941</ref> <ref>PMID:18264132</ref> <ref>PMID:20127681</ref> <ref>PMID:20375222</ref> <ref>PMID:20837705</ref> <ref>PMID:21170385</ref> <ref>PMID:20657822</ref> <ref>PMID:21589879</ref> <ref>PMID:21730191</ref> <ref>PMID:21883093</ref> <ref>PMID:22034099</ref> <ref>PMID:22323517</ref> <ref>PMID:22872150</ref>	+	[https://www.uniprot.org/uniprot/DDX3X_HUMAN DDX3X_HUMAN] Multifunctional ATP-dependent RNA helicase. The ATPase activity can be stimulated by various ribo- and deoxynucleic acids indicative for a relaxed substrate specificity. In vitro can unwind partially double stranded DNA with a preference for 5'-single stranded DNA overhangs. Is involved in several steps of gene expression, such as transcription, mRNA maturation, mRNA export and translation. However, the exact mechanisms are not known and some functions may be specific for a subset of mRNAs. Involved in transcriptional regulation. Can enhance transcription from the CDKN1A/WAF1 promoter in a SP1-dependent manner. Found associated with the E-cadherin promoter and can down-regulate transcription from the promoter. Involved in regulation of translation initiation. Proposed to be involved in positive regulation of translation such as of cyclin E1/CCNE1 mRNA and specifically of mRNAs containing complex secondary structures in their 5'UTRs; these functions seem to require RNA helicase activity. Specifically promotes translation of a subset of viral and cellular mRNAs carrying a 5'proximal stem-loop structure in their 5'UTRs and cooperates with the eIF4F complex. Proposed to act prior to 43S ribosomal scanning and to locally destabilize these RNA structures to allow recognition of the mRNA cap or loading onto the 40S subunit. After association with 40S ribosomal subunits seems to be involved in the functional assembly of 80S ribosomes; the function seems to cover translation of mRNAs with structured and non-structured 5'UTRs and is independent of RNA helicase activity. Also proposed to inhibit cap-dependent translation by competetive interaction with EIF4E which can block the EIF4E:EIF4G complex formation. Proposed to be involved in stress response and stress granule assembly; the function is independent of RNA helicase activity and seems to involve association with EIF4E. May be involved in nuclear export of specific mRNAs but not in bulk mRNA export via interactions with XPO1 and NXF1. Also associates with polyadenylated mRNAs independently of NXF1. Associates with spliced mRNAs in an exon junction complex (EJC)-dependent manner and seems not to be directly involved in splicing. May be involved in nuclear mRNA export by association with DDX5 and regulating its nuclear location. Involved in innate immune signaling promoting the production of type I interferon (IFN-alpha and IFN-beta); proposed to act as viral RNA sensor, signaling intermediate and transcriptional coactivator. Involved in TBK1 and IKBKE-dependent IRF3 activation leading to IFN-beta induction. Also found associated with IFN-beta promoters; the function is independent of IRF3. Can bind to viral RNAs and via association with MAVS/IPS1 and DDX58/RIG-I is thought to induce signaling in early stages of infection. Involved in regulation of apoptosis. May be required for activation of the intrinsic but inhibit activation of the extrinsic apoptotic pathway. Acts as an antiapoptotic protein through association with GSK3A/B and BIRC2 in an apoptosis antagonizing signaling complex; activation of death receptors promotes caspase-dependent cleavage of BIRC2 and DDX3X and relieves the inhibition. May be involved in mitotic chromosome segregation. Appears to be a prime target for viral manipulations. Hepatitis B virus (HBV) polymerase and possibly vaccinia virus (VACV) protein K7 inhibit IFN-beta induction probably by dissociating DDX3X from TBK1 or IKBKE. Is involved in hepatitis C virus (HCV) replication; the function may involve the association with HCV core protein. HCV core protein inhibits the IPS1-dependent function in viral RNA sensing and may switch the function from a INF-beta inducing to a HCV replication mode. Involved in HIV-1 replication. Acts as a cofactor for XPO1-mediated nuclear export of incompletely spliced HIV-1 Rev RNAs.<ref>PMID:10329544</ref> <ref>PMID:15507209</ref> <ref>PMID:16818630</ref> <ref>PMID:16301996</ref> <ref>PMID:17357160</ref> <ref>PMID:18846110</ref> <ref>PMID:18583960</ref> <ref>PMID:18636090</ref> <ref>PMID:18596238</ref> <ref>PMID:18628297</ref> <ref>PMID:17667941</ref> <ref>PMID:18264132</ref> <ref>PMID:20127681</ref> <ref>PMID:20375222</ref> <ref>PMID:20837705</ref> <ref>PMID:21170385</ref> <ref>PMID:20657822</ref> <ref>PMID:21589879</ref> <ref>PMID:21730191</ref> <ref>PMID:21883093</ref> <ref>PMID:22034099</ref> <ref>PMID:22323517</ref> <ref>PMID:22872150</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4px9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4px9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~RNA helicase~~]]	+	[[Category: Large Structures]]
-	[[Category: Enemark~~, E J~~]]	+	[[Category: Enemark EJ]]
-	[[Category: Epling~~, L B~~]]	+	[[Category: Epling LB]]
-	[[Category: Grace~~, C R~~]]	+	[[Category: Grace CR]]
-	[[Category: Lowe~~, B R~~]]	+	[[Category: Lowe BR]]
-	[[Category: Partridge~~, J F]]~~	+	[[Category: Partridge JF]]
-	~~[[Category: Dead-box helicase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 08:46, 22 November 2017

OCA — Wed, 22 Nov 2017 08:46:14 GMT

←Older revision		Revision as of 08:46, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4px9' size='340' side='right' caption='[[4px9]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='4px9' size='340' side='right' caption='[[4px9]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4px9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4px9]] is a 3 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=4PX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PX9 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxa\|4pxa]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxa\|4pxa]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DBX, DDX3, DDX3X ([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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [http://pdbe.org/4px9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [http://www.ebi.ac.uk/pdbsum/4px9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4px9 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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [http://pdbe.org/4px9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [http://www.ebi.ac.uk/pdbsum/4px9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4px9 ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Enemark, E J]]		[[Category: Enemark, E J]]

OCA at 18:48, 1 February 2017

OCA — Wed, 01 Feb 2017 18:48:59 GMT

←Older revision		Revision as of 18:48, 1 February 2017
Line 1:		Line 1:
		+
	==DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop==		==DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop==
	<StructureSection load='4px9' size='340' side='right' caption='[[4px9]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='4px9' size='340' side='right' caption='[[4px9]], [[Resolution\|resolution]] 2.31Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxa\|4pxa]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxa\|4pxa]]</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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [http://www.ebi.ac.uk/pdbsum/4px9 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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [http://pdbe.org/4px9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [http://www.ebi.ac.uk/pdbsum/4px9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4px9 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 4px9" style="background-color:#fffaf0;"></div>
-	==~~See Also==~~	+
-	*[[Helicase\|Helicase]]	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:43, 30 April 2015

OCA — Thu, 30 Apr 2015 05:43:15 GMT

←Older revision		Revision as of 05:43, 30 April 2015
Line 18:		Line 18:
	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>
		+
		+	==See Also==
		+	*[[Helicase\|Helicase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:48, 11 March 2015

OCA — Wed, 11 Mar 2015 11:48:40 GMT

←Older revision		Revision as of 11:48, 11 March 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop==
		+	<StructureSection load='4px9' size='340' side='right' caption='[[4px9]], [[Resolution\|resolution]] 2.31Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4px9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PX9 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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxa\|4pxa]]</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=4px9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4px9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4px9 RCSB], [http://www.ebi.ac.uk/pdbsum/4px9 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDX3X_HUMAN DDX3X_HUMAN]] Multifunctional ATP-dependent RNA helicase. The ATPase activity can be stimulated by various ribo- and deoxynucleic acids indicative for a relaxed substrate specificity. In vitro can unwind partially double stranded DNA with a preference for 5'-single stranded DNA overhangs. Is involved in several steps of gene expression, such as transcription, mRNA maturation, mRNA export and translation. However, the exact mechanisms are not known and some functions may be specific for a subset of mRNAs. Involved in transcriptional regulation. Can enhance transcription from the CDKN1A/WAF1 promoter in a SP1-dependent manner. Found associated with the E-cadherin promoter and can down-regulate transcription from the promoter. Involved in regulation of translation initiation. Proposed to be involved in positive regulation of translation such as of cyclin E1/CCNE1 mRNA and specifically of mRNAs containing complex secondary structures in their 5'UTRs; these functions seem to require RNA helicase activity. Specifically promotes translation of a subset of viral and cellular mRNAs carrying a 5'proximal stem-loop structure in their 5'UTRs and cooperates with the eIF4F complex. Proposed to act prior to 43S ribosomal scanning and to locally destabilize these RNA structures to allow recognition of the mRNA cap or loading onto the 40S subunit. After association with 40S ribosomal subunits seems to be involved in the functional assembly of 80S ribosomes; the function seems to cover translation of mRNAs with structured and non-structured 5'UTRs and is independent of RNA helicase activity. Also proposed to inhibit cap-dependent translation by competetive interaction with EIF4E which can block the EIF4E:EIF4G complex formation. Proposed to be involved in stress response and stress granule assembly; the function is independent of RNA helicase activity and seems to involve association with EIF4E. May be involved in nuclear export of specific mRNAs but not in bulk mRNA export via interactions with XPO1 and NXF1. Also associates with polyadenylated mRNAs independently of NXF1. Associates with spliced mRNAs in an exon junction complex (EJC)-dependent manner and seems not to be directly involved in splicing. May be involved in nuclear mRNA export by association with DDX5 and regulating its nuclear location. Involved in innate immune signaling promoting the production of type I interferon (IFN-alpha and IFN-beta); proposed to act as viral RNA sensor, signaling intermediate and transcriptional coactivator. Involved in TBK1 and IKBKE-dependent IRF3 activation leading to IFN-beta induction. Also found associated with IFN-beta promoters; the function is independent of IRF3. Can bind to viral RNAs and via association with MAVS/IPS1 and DDX58/RIG-I is thought to induce signaling in early stages of infection. Involved in regulation of apoptosis. May be required for activation of the intrinsic but inhibit activation of the extrinsic apoptotic pathway. Acts as an antiapoptotic protein through association with GSK3A/B and BIRC2 in an apoptosis antagonizing signaling complex; activation of death receptors promotes caspase-dependent cleavage of BIRC2 and DDX3X and relieves the inhibition. May be involved in mitotic chromosome segregation. Appears to be a prime target for viral manipulations. Hepatitis B virus (HBV) polymerase and possibly vaccinia virus (VACV) protein K7 inhibit IFN-beta induction probably by dissociating DDX3X from TBK1 or IKBKE. Is involved in hepatitis C virus (HCV) replication; the function may involve the association with HCV core protein. HCV core protein inhibits the IPS1-dependent function in viral RNA sensing and may switch the function from a INF-beta inducing to a HCV replication mode. Involved in HIV-1 replication. Acts as a cofactor for XPO1-mediated nuclear export of incompletely spliced HIV-1 Rev RNAs.<ref>PMID:10329544</ref> <ref>PMID:15507209</ref> <ref>PMID:16818630</ref> <ref>PMID:16301996</ref> <ref>PMID:17357160</ref> <ref>PMID:18846110</ref> <ref>PMID:18583960</ref> <ref>PMID:18636090</ref> <ref>PMID:18596238</ref> <ref>PMID:18628297</ref> <ref>PMID:17667941</ref> <ref>PMID:18264132</ref> <ref>PMID:20127681</ref> <ref>PMID:20375222</ref> <ref>PMID:20837705</ref> <ref>PMID:21170385</ref> <ref>PMID:20657822</ref> <ref>PMID:21589879</ref> <ref>PMID:21730191</ref> <ref>PMID:21883093</ref> <ref>PMID:22034099</ref> <ref>PMID:22323517</ref> <ref>PMID:22872150</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The DEAD-box RNA helicase DDX3X is frequently mutated in pediatric medulloblastoma. We dissect how these mutants affect DDX3X function with structural, biochemical, and genetic experiments. We identify an N-terminal extension ("ATP-binding loop", ABL) that is critical for the stimulation of ATP hydrolysis by RNA. We present crystal structures suggesting that the ABL interacts dynamically with ATP and confirming that the interaction occurs in solution by NMR chemical shift perturbation and isothermal titration calorimetry. DEAD-box helicases require interaction between two conserved RecA-like helicase domains, D1 and D2 for function. We use NMR chemical shift perturbation to show that DDX3X interacts specifically with double-stranded RNA through its D1 domain, with contact mediated by residues G302 and G325. Mutants of these residues, G302V and G325E, are associated with pediatric medulloblastoma. These mutants are defective in RNA-stimulated ATP hydrolysis. We show that DDX3X complements the growth defect in a ded1 temperature-sensitive strain of Schizosaccharomyces pombe, but the cancer-associated mutants G302V and G325E do not complement and exhibit protein expression defects. Taken together, our results suggest that impaired translation of important mRNA targets by mutant DDX3X represents a key step in the development of medulloblastoma.

-	~~The entry 4px9 is ON HOLD until Mar~~ 25 ~~2016~~	+	Cancer-Associated Mutants of RNA Helicase DDX3X Are Defective in RNA-Stimulated ATP Hydrolysis.,Epling LB, Grace CR, Lowe BR, Partridge JF, Enemark EJ J Mol Biol. 2015 Feb 25. pii: S0022-2836(15)00109-6. doi:, 10.1016/j.jmb.2015.02.015. PMID:25724843<ref>PMID:25724843</ref>

-	~~Authors: Epling~~, L.B.~~, Grace, C.R., Lowe, B.R., Partridge, J.F., Enemark, E.J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~DDX3X D1 with ATP-binding Loop~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: Epling, L.B]]	+	__TOC__
-	[[Category: Grace, C.R]]	+	</StructureSection>
-	[[Category: Partridge, J.F]]	+	[[Category: RNA helicase]]
-	[[Category: ~~Lowe, B.R~~]]	+	[[Category: Enemark, E J]]
-	[[Category: ~~Enemark, E.J~~]]	+	[[Category: Epling, L B]]
		+	[[Category: Grace, C R]]
		+	[[Category: Lowe, B R]]
		+	[[Category: Partridge, J F]]
		+	[[Category: Dead-box helicase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Translation]]

OCA at 07:12, 4 March 2015

OCA — Wed, 04 Mar 2015 07:12:50 GMT

←Older revision		Revision as of 07:12, 4 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4px9 is ON HOLD until ~~Paper Publication~~	+	The entry 4px9 is ON HOLD until Mar 25 2016

	Authors: Epling, L.B., Grace, C.R., Lowe, B.R., Partridge, J.F., Enemark, E.J.		Authors: Epling, L.B., Grace, C.R., Lowe, B.R., Partridge, J.F., Enemark, E.J.

OCA at 15:17, 24 December 2014

OCA — Wed, 24 Dec 2014 15:17:53 GMT

←Older revision		Revision as of 15:17, 24 December 2014
Line 6:		Line 6:

	Description: DDX3X D1 with ATP-binding Loop		Description: DDX3X D1 with ATP-binding Loop
		+	[[Category: Unreleased Structures]]
		+	[[Category: Epling, L.B]]
		+	[[Category: Grace, C.R]]
		+	[[Category: Partridge, J.F]]
		+	[[Category: Lowe, B.R]]
		+	[[Category: Enemark, E.J]]

OCA at 07:27, 23 April 2014

OCA — Wed, 23 Apr 2014 07:27:46 GMT

←Older revision		Revision as of 07:27, 23 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4px9 is ON HOLD	+	The entry 4px9 is ON HOLD until Paper Publication

	Authors: Epling, L.B., Grace, C.R., Lowe, B.R., Partridge, J.F., Enemark, E.J.		Authors: Epling, L.B., Grace, C.R., Lowe, B.R., Partridge, J.F., Enemark, E.J.

	Description: DDX3X D1 with ATP-binding Loop		Description: DDX3X D1 with ATP-binding Loop

OCA at 05:57, 9 April 2014

OCA — Wed, 09 Apr 2014 05:57:36 GMT

←Older revision		Revision as of 05:57, 9 April 2014
Line 3:		Line 3:
	The entry 4px9 is ON HOLD		The entry 4px9 is ON HOLD

-	Authors: Epling, L.B., Grace, C.R., Lowe, B. R., Partridge, J.F., Enemark, E.J.	+	Authors: Epling, L.B., Grace, C.R., Lowe, B.R., Partridge, J.F., Enemark, E.J.

	Description: DDX3X D1 with ATP-binding Loop		Description: DDX3X D1 with ATP-binding Loop