3ts9 - Revision history

OCA at 10:11, 1 March 2024

OCA — Fri, 01 Mar 2024 10:11:09 GMT

←Older revision		Revision as of 10:11, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3ts9' size='340' side='right'caption='[[3ts9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3ts9' size='340' side='right'caption='[[3ts9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.003Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Ifih1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~10090 LK3 transgenic mice])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [https://pdbe.org/3ts9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ts9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ts9 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=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [https://pdbe.org/3ts9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ts9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ts9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/IFIH1_MOUSE IFIH1_MOUSE]] Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include mRNA lacking 2'-O-methylation at their 5' cap and long-dsRNA (>1 kb in length). Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Responsible for detecting the Picornaviridae family members such as encephalomyocarditis virus (EMCV), mengo encephalomyocarditis virus (ENMG), and theiler's murine encephalomyelitis virus (TMEV). Can also detect other viruses such as dengue virus (DENV), west Nile virus (WNV), and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome, such as vaccinia virus. Plays an important role in amplifying innate immune signaling through recognition of RNA metabolites that are produced during virus infection by ribonuclease L (RNase L). May play an important role in enhancing natural killer cell function and may be involved in growth inhibition and apoptosis in several tumor cell lines.<ref>PMID:12015121</ref> <ref>PMID:16625202</ref> <ref>PMID:17942531</ref> <ref>PMID:19656871</ref> <ref>PMID:21217758</ref>	+	[https://www.uniprot.org/uniprot/IFIH1_MOUSE IFIH1_MOUSE] Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include mRNA lacking 2'-O-methylation at their 5' cap and long-dsRNA (>1 kb in length). Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Responsible for detecting the Picornaviridae family members such as encephalomyocarditis virus (EMCV), mengo encephalomyocarditis virus (ENMG), and theiler's murine encephalomyelitis virus (TMEV). Can also detect other viruses such as dengue virus (DENV), west Nile virus (WNV), and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome, such as vaccinia virus. Plays an important role in amplifying innate immune signaling through recognition of RNA metabolites that are produced during virus infection by ribonuclease L (RNase L). May play an important role in enhancing natural killer cell function and may be involved in growth inhibition and apoptosis in several tumor cell lines.<ref>PMID:12015121</ref> <ref>PMID:16625202</ref> <ref>PMID:17942531</ref> <ref>PMID:19656871</ref> <ref>PMID:21217758</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Melanoma differentiation-associated gene-5 (MDA5) detects viral double-stranded RNA in the cytoplasm. RNA binding induces MDA5 to activate the signalling adaptor MAVS through interactions between the caspase recruitment domains (CARDs) of the two proteins. The molecular mechanism of MDA5 signalling is not well understood. Here, we show that MDA5 cooperatively binds short RNA ligands as a dimer with a 16-18-basepair footprint. A crystal structure of the MDA5 helicase-insert domain demonstrates an evolutionary relationship with the archaeal Hef helicases. In X-ray solution structures, the CARDs in unliganded MDA5 are flexible, and RNA binds on one side of an asymmetric MDA5 dimer, bridging the two subunits. On longer RNA, full-length and CARD-deleted MDA5 constructs assemble into ATP-sensitive filaments. We propose a signalling model in which the CARDs on MDA5-RNA filaments nucleate the assembly of MAVS filaments with the same polymeric geometry.	+
-		+
-	~~MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA.,Berke IC, Modis Y EMBO J. 2012 Feb 7. doi: 10.1038/emboj.2012.19. PMID:22314235<ref>PMID:22314235</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3ts9" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 15:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice]]~~	+	[[Category: Mus musculus]]
-	~~[[Category: RNA helicase~~]]	+	[[Category: Berke IC]]
-	[[Category: Berke~~, I C~~]]	+	[[Category: Modis Y]]
-	[[Category: Modis, Y]]	+
-	~~[[Category: Antiviral protein]]~~	+
-	~~[[Category: Dexd/h helicase]]~~	+
-	~~[[Category: Fancm helicase]]~~	+
-	~~[[Category: Helix bundle]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rig-i-like helicase]]~~	+
-	~~[[Category: Sf2 helicase]]~~	+
-	~~[[Category: Super family 2 helicase~~]]	+

OCA at 05:43, 13 July 2022

OCA — Wed, 13 Jul 2022 05:43:09 GMT

←Older revision		Revision as of 05:43, 13 July 2022
Line 1:		Line 1:

	==Crystal Structure of the MDA5 Helicase Insert Domain==		==Crystal Structure of the MDA5 Helicase Insert Domain==
-	<StructureSection load='3ts9' size='340' side='right' caption='[[3ts9]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3ts9' size='340' side='right'caption='[[3ts9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ifih1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ifih1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [~~http~~://pdbe.org/3ts9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ts9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ts9 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=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [https://pdbe.org/3ts9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ts9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ts9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/IFIH1_MOUSE IFIH1_MOUSE]] Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include mRNA lacking 2'-O-methylation at their 5' cap and long-dsRNA (>1 kb in length). Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Responsible for detecting the Picornaviridae family members such as encephalomyocarditis virus (EMCV), mengo encephalomyocarditis virus (ENMG), and theiler's murine encephalomyelitis virus (TMEV). Can also detect other viruses such as dengue virus (DENV), west Nile virus (WNV), and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome, such as vaccinia virus. Plays an important role in amplifying innate immune signaling through recognition of RNA metabolites that are produced during virus infection by ribonuclease L (RNase L). May play an important role in enhancing natural killer cell function and may be involved in growth inhibition and apoptosis in several tumor cell lines.<ref>PMID:12015121</ref> <ref>PMID:16625202</ref> <ref>PMID:17942531</ref> <ref>PMID:19656871</ref> <ref>PMID:21217758</ref>	+	[[https://www.uniprot.org/uniprot/IFIH1_MOUSE IFIH1_MOUSE]] Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include mRNA lacking 2'-O-methylation at their 5' cap and long-dsRNA (>1 kb in length). Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Responsible for detecting the Picornaviridae family members such as encephalomyocarditis virus (EMCV), mengo encephalomyocarditis virus (ENMG), and theiler's murine encephalomyelitis virus (TMEV). Can also detect other viruses such as dengue virus (DENV), west Nile virus (WNV), and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome, such as vaccinia virus. Plays an important role in amplifying innate immune signaling through recognition of RNA metabolites that are produced during virus infection by ribonuclease L (RNase L). May play an important role in enhancing natural killer cell function and may be involved in growth inhibition and apoptosis in several tumor cell lines.<ref>PMID:12015121</ref> <ref>PMID:16625202</ref> <ref>PMID:17942531</ref> <ref>PMID:19656871</ref> <ref>PMID:21217758</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]

OCA at 12:23, 11 August 2016

OCA — Thu, 11 Aug 2016 12:23:21 GMT

←Older revision		Revision as of 12:23, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the MDA5 Helicase Insert Domain==		==Crystal Structure of the MDA5 Helicase Insert Domain==
	<StructureSection load='3ts9' size='340' side='right' caption='[[3ts9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3ts9' size='340' side='right' caption='[[3ts9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ifih1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 ~~Mus musculus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ifih1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ts9 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=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [http://pdbe.org/3ts9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ts9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ts9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IFIH1_MOUSE IFIH1_MOUSE]] Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include mRNA lacking 2'-O-methylation at their 5' cap and long-dsRNA (>1 kb in length). Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Responsible for detecting the Picornaviridae family members such as encephalomyocarditis virus (EMCV), mengo encephalomyocarditis virus (ENMG), and theiler's murine encephalomyelitis virus (TMEV). Can also detect other viruses such as dengue virus (DENV), west Nile virus (WNV), and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome, such as vaccinia virus. Plays an important role in amplifying innate immune signaling through recognition of RNA metabolites that are produced during virus infection by ribonuclease L (RNase L). May play an important role in enhancing natural killer cell function and may be involved in growth inhibition and apoptosis in several tumor cell lines.<ref>PMID:12015121</ref> <ref>PMID:16625202</ref> <ref>PMID:17942531</ref> <ref>PMID:19656871</ref> <ref>PMID:21217758</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		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 3ts9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Berke, I C]]		[[Category: Berke, I C]]

OCA at 11:08, 4 January 2015

OCA — Sun, 04 Jan 2015 11:08:55 GMT

←Older revision		Revision as of 11:08, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ifih1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ifih1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ts9 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=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ts9 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA.,Berke IC, Modis Y EMBO J. 2012 Feb 7. doi: 10.1038/emboj.2012.19. PMID:22314235<ref>PMID:22314235</ref>		MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA.,Berke IC, Modis Y EMBO J. 2012 Feb 7. doi: 10.1038/emboj.2012.19. PMID:22314235<ref>PMID:22314235</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 22:		Line 22:
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
-	[[Category: Berke, I C.]]	+	[[Category: Berke, I C]]
-	[[Category: Modis, Y.]]	+	[[Category: Modis, Y]]
	[[Category: Antiviral protein]]		[[Category: Antiviral protein]]
	[[Category: Dexd/h helicase]]		[[Category: Dexd/h helicase]]

OCA at 06:45, 5 June 2014

OCA — Thu, 05 Jun 2014 06:45:47 GMT

←Older revision		Revision as of 06:45, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3ts9.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of the MDA5 Helicase Insert Domain==
		+	<StructureSection load='3ts9' size='340' side='right' caption='[[3ts9]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ts9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TS9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ifih1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ts9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ts9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ts9 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Melanoma differentiation-associated gene-5 (MDA5) detects viral double-stranded RNA in the cytoplasm. RNA binding induces MDA5 to activate the signalling adaptor MAVS through interactions between the caspase recruitment domains (CARDs) of the two proteins. The molecular mechanism of MDA5 signalling is not well understood. Here, we show that MDA5 cooperatively binds short RNA ligands as a dimer with a 16-18-basepair footprint. A crystal structure of the MDA5 helicase-insert domain demonstrates an evolutionary relationship with the archaeal Hef helicases. In X-ray solution structures, the CARDs in unliganded MDA5 are flexible, and RNA binds on one side of an asymmetric MDA5 dimer, bridging the two subunits. On longer RNA, full-length and CARD-deleted MDA5 constructs assemble into ATP-sensitive filaments. We propose a signalling model in which the CARDs on MDA5-RNA filaments nucleate the assembly of MAVS filaments with the same polymeric geometry.

-	<!--	+	MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA.,Berke IC, Modis Y EMBO J. 2012 Feb 7. doi: 10.1038/emboj.2012.19. PMID:22314235<ref>PMID:22314235</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3ts9"~~, ~~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_3ts9\| PDB=3ts9 \| SCENE= }}~~	+

-	~~===Crystal Structure~~ of the ~~MDA5 Helicase Insert Domain===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22314235}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22314235 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22314235}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ts9]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022314235<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]

OCA at 08:51, 29 February 2012

OCA — Wed, 29 Feb 2012 08:51:04 GMT

←Older revision		Revision as of 08:51, 29 February 2012
Line 1:		Line 1:
-	[[Image:3ts9.~~jpg~~\|left\|200px]]	+	[[Image:3ts9.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal Structure of the MDA5 Helicase Insert Domain===		===Crystal Structure of the MDA5 Helicase Insert Domain===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22314235}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22314235 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22314235}}

	==About this Structure==		==About this Structure==

OCA at 07:52, 22 February 2012

OCA — Wed, 22 Feb 2012 07:52:01 GMT

←Older revision		Revision as of 07:52, 22 February 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ts9.jpg\|left\|200px]]

-	The ~~entry 3ts9~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ts9", 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_3ts9\| PDB=3ts9 \| SCENE= }}

-	~~Authors: Berke, I.C., Modis, Y.~~	+	===Crystal Structure of the MDA5 Helicase Insert Domain===

-	~~Description: Crystal~~ Structure ~~of the MDA5 Helicase Insert Domain~~	+
		+	==About this Structure==
		+	[[3ts9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TS9 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022314235</ref><references group="xtra"/>
		+	[[Category: Mus musculus]]
		+	[[Category: RNA helicase]]
		+	[[Category: Berke, I C.]]
		+	[[Category: Modis, Y.]]
		+	[[Category: Antiviral protein]]
		+	[[Category: Dexd/h helicase]]
		+	[[Category: Fancm helicase]]
		+	[[Category: Helix bundle]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rig-i-like helicase]]
		+	[[Category: Sf2 helicase]]
		+	[[Category: Super family 2 helicase]]

OCA at 05:16, 28 September 2011

OCA — Wed, 28 Sep 2011 05:16:29 GMT

←Older revision		Revision as of 05:16, 28 September 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ts9 is ON HOLD	+	The entry 3ts9 is ON HOLD until Paper Publication

-	Authors: Berke, I.C., Modis, Y.E.	+	Authors: Berke, I.C., Modis, Y.

	Description: Crystal Structure of the MDA5 Helicase Insert Domain		Description: Crystal Structure of the MDA5 Helicase Insert Domain

OCA: Protected "3ts9" [edit=sysop:move=sysop]

OCA — Wed, 21 Sep 2011 05:33:42 GMT

Protected "3ts9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:33, 21 September 2011

OCA: New page: '''Unreleased structure''' The entry 3ts9 is ON HOLD Authors: Berke, I.C., Modis, Y.E. Description: Crystal Structure of the MDA5 Helicase Insert Domain

OCA — Wed, 21 Sep 2011 05:33:41 GMT

New page: '''Unreleased structure''' The entry 3ts9 is ON HOLD Authors: Berke, I.C., Modis, Y.E. Description: Crystal Structure of the MDA5 Helicase Insert Domain

New page

'''Unreleased structure'''

The entry 3ts9 is ON HOLD

Authors: Berke, I.C., Modis, Y.E.

Description: Crystal Structure of the MDA5 Helicase Insert Domain