2qfd - Revision history

OCA at 08:18, 25 June 2021

OCA — Fri, 25 Jun 2021 08:18:15 GMT

←Older revision		Revision as of 08:18, 25 June 2021
Line 1:		Line 1:

	==Crystal structure of the regulatory domain of human RIG-I with bound Hg==		==Crystal structure of the regulatory domain of human RIG-I with bound Hg==
-	<StructureSection load='2qfd' size='340' side='right' caption='[[2qfd]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2qfd' size='340' side='right'caption='[[2qfd]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qfd]] is a 10 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=2QFD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QFD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qfd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QFD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qfb\|2qfb]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX58 ([~~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">DDX58 ([https://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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [~~http~~://pdbe.org/2qfd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qfd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfd 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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [https://pdbe.org/2qfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [https://www.ebi.ac.uk/pdbsum/2qfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DDX58_HUMAN DDX58_HUMAN]] 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: 5'-triphosphorylated ssRNA and dsRNA and short dsRNA (<1 kb in length). In addition to the 5'-triphosphate moiety, blunt-end base pairing at the 5'-end of the RNA is very essential. Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity. A 3'overhang at the 5'triphosphate end decreases and any 5'overhang at the 5' triphosphate end abolishes its activity. 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. Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: Human respiratory syncytial virus and measles virus (MeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV). It also detects rotavirus and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration.<ref>PMID:15208624</ref> <ref>PMID:16125763</ref> <ref>PMID:15708988</ref> <ref>PMID:16153868</ref> <ref>PMID:16127453</ref> <ref>PMID:17190814</ref> <ref>PMID:18636086</ref> <ref>PMID:19631370</ref> <ref>PMID:19576794</ref> <ref>PMID:19122199</ref> <ref>PMID:19211564</ref> <ref>PMID:19609254</ref> <ref>PMID:21742966</ref>	+	[[https://www.uniprot.org/uniprot/DDX58_HUMAN DDX58_HUMAN]] 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: 5'-triphosphorylated ssRNA and dsRNA and short dsRNA (<1 kb in length). In addition to the 5'-triphosphate moiety, blunt-end base pairing at the 5'-end of the RNA is very essential. Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity. A 3'overhang at the 5'triphosphate end decreases and any 5'overhang at the 5' triphosphate end abolishes its activity. 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. Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: Human respiratory syncytial virus and measles virus (MeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV). It also detects rotavirus and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration.<ref>PMID:15208624</ref> <ref>PMID:16125763</ref> <ref>PMID:15708988</ref> <ref>PMID:16153868</ref> <ref>PMID:16127453</ref> <ref>PMID:17190814</ref> <ref>PMID:18636086</ref> <ref>PMID:19631370</ref> <ref>PMID:19576794</ref> <ref>PMID:19122199</ref> <ref>PMID:19211564</ref> <ref>PMID:19609254</ref> <ref>PMID:21742966</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cui, S]]		[[Category: Cui, S]]
	[[Category: Hopfner, K P]]		[[Category: Hopfner, K P]]

OCA at 08:17, 29 August 2018

OCA — Wed, 29 Aug 2018 08:17:35 GMT

←Older revision		Revision as of 08:17, 29 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of the regulatory domain of human RIG-I with bound Hg==		==Crystal structure of the regulatory domain of human RIG-I with bound Hg==
	<StructureSection load='2qfd' size='340' side='right' caption='[[2qfd]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2qfd' size='340' side='right' caption='[[2qfd]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX58 ([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">DDX58 ([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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [http://pdbe.org/2qfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [http://www.ebi.ac.uk/pdbsum/2qfd 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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [http://pdbe.org/2qfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [http://www.ebi.ac.uk/pdbsum/2qfd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfd 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/qf/2qfd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qf/2qfd_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>
Line 38:		Line 39:
	[[Category: Lammens, A]]		[[Category: Lammens, A]]
	[[Category: Lammens, K]]		[[Category: Lammens, K]]
		+	[[Category: Alternative splicing]]
	[[Category: Antiviral defense]]		[[Category: Antiviral defense]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
Line 46:		Line 48:
	[[Category: Interferon induction]]		[[Category: Interferon induction]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
		+	[[Category: Polymorphism]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
		+	[[Category: Ubl conjugation]]
	[[Category: Zinc finger]]		[[Category: Zinc finger]]

OCA at 02:10, 9 February 2016

OCA — Tue, 09 Feb 2016 02:10:31 GMT

←Older revision		Revision as of 02:10, 9 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=2qfd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:35, 10 September 2015

OCA — Thu, 10 Sep 2015 17:35:35 GMT

←Older revision		Revision as of 17:35, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2qfd' size='340' side='right' caption='[[2qfd]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2qfd' size='340' side='right' caption='[[2qfd]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qfd]] is a 10 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=2QFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qfd]] is a 10 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=2QFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX58 ([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">DDX58 ([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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [http://www.ebi.ac.uk/pdbsum/2qfd 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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [http://pdbe.org/2qfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [http://www.ebi.ac.uk/pdbsum/2qfd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 2qfd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cui, S]]		[[Category: Cui, S]]
	[[Category: Hopfner, K P]]		[[Category: Hopfner, K P]]

OCA at 03:41, 25 December 2014

OCA — Thu, 25 Dec 2014 03:41:55 GMT

←Older revision		Revision as of 03:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qfd]] is a 10 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=2QFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qfd]] is a 10 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=2QFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX58 ([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">DDX58 ([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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [http://www.ebi.ac.uk/pdbsum/2qfd 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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [http://www.ebi.ac.uk/pdbsum/2qfd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDX58_HUMAN DDX58_HUMAN]] 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: 5'-triphosphorylated ssRNA and dsRNA and short dsRNA (<1 kb in length). In addition to the 5'-triphosphate moiety, blunt-end base pairing at the 5'-end of the RNA is very essential. Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity. A 3'overhang at the 5'triphosphate end decreases and any 5'overhang at the 5' triphosphate end abolishes its activity. 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. Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: Human respiratory syncytial virus and measles virus (MeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV). It also detects rotavirus and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration.<ref>PMID:15208624</ref> <ref>PMID:16125763</ref> <ref>PMID:15708988</ref> <ref>PMID:16153868</ref> <ref>PMID:16127453</ref> <ref>PMID:17190814</ref> <ref>PMID:18636086</ref> <ref>PMID:19631370</ref> <ref>PMID:19576794</ref> <ref>PMID:19122199</ref> <ref>PMID:19211564</ref> <ref>PMID:19609254</ref> <ref>PMID:21742966</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: Cui, S.]]	+	[[Category: Cui, S]]
-	[[Category: Hopfner, K P.]]	+	[[Category: Hopfner, K P]]
-	[[Category: Lammens, A.]]	+	[[Category: Lammens, A]]
-	[[Category: Lammens, K.]]	+	[[Category: Lammens, K]]
	[[Category: Antiviral defense]]		[[Category: Antiviral defense]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 19:12, 30 September 2014

OCA — Tue, 30 Sep 2014 19:12:18 GMT

←Older revision		Revision as of 19:12, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qfd.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the regulatory domain of human RIG-I with bound Hg==
		+	<StructureSection load='2qfd' size='340' side='right' caption='[[2qfd]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qfd]] is a 10 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=2QFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfb\|2qfb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX58 ([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=2qfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfd RCSB], [http://www.ebi.ac.uk/pdbsum/2qfd 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/qf/2qfd_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 ==
		+	The ATPase RIG-I senses viral RNAs that contain 5'-triphosphates in the cytoplasm. It initiates a signaling cascade that activates innate immune response by interferon and cytokine production, providing essential antiviral protection for the host. The mode of RNA 5'-triphosphate sensing by RIG-I remains elusive. We show that the C-terminal regulatory domain RD of RIG-I binds viral RNA in a 5'-triphosphate-dependent manner and activates the RIG-I ATPase by RNA-dependent dimerization. The crystal structure of RD reveals a zinc-binding domain that is structurally related to GDP/GTP exchange factors of Rab-like GTPases. The zinc coordination site is essential for RIG-I signaling and is also conserved in MDA5 and LGP2, suggesting related RD domains in all three enzymes. Structure-guided mutagenesis identifies a positively charged groove as likely 5'-triphosphate-binding site of RIG-I. This groove is distinct in MDA5 and LGP2, raising the possibility that RD confers ligand specificity.

-	~~{{STRUCTURE_2qfd\| PDB=2qfd \| SCENE= }}~~	+	The C-terminal regulatory domain is the RNA 5'-triphosphate sensor of RIG-I.,Cui S, Eisenacher K, Kirchhofer A, Brzozka K, Lammens A, Lammens K, Fujita T, Conzelmann KK, Krug A, Hopfner KP Mol Cell. 2008 Feb 1;29(2):169-79. PMID:18243112<ref>PMID:18243112</ref>

-	~~===Crystal structure~~ of the ~~regulatory domain of human RIG-I with bound Hg===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18243112}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2qfd]] is a 10 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=2QFD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018243112<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cui, S.]]		[[Category: Cui, S.]]

OCA: Protected "2qfd" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:13:41 GMT

Protected "2qfd" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:13, 7 January 2013

OCA at 19:13, 7 January 2013

OCA — Mon, 07 Jan 2013 19:13:38 GMT

←Older revision		Revision as of 19:13, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2qfd.png\|left\|200px]]		[[Image:2qfd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qfd", 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.
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	{{STRUCTURE_2qfd\| PDB=2qfd \| SCENE= }}		{{STRUCTURE_2qfd\| PDB=2qfd \| SCENE= }}

	===Crystal structure of the regulatory domain of human RIG-I with bound Hg===		===Crystal structure of the regulatory domain of human RIG-I with bound Hg===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18243112}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18243112 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18243112}}		{{ABSTRACT_PUBMED_18243112}}

	==About this Structure==		==About this Structure==
-	~~2QFD~~ is a 10 ~~chains~~ structure ~~of sequences~~ 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=2QFD OCA].	+	[[2qfd]] is a 10 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=2QFD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18243112~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018243112</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cui, S.]]		[[Category: Cui, S.]]
Line 29:		Line 17:
	[[Category: Lammens, A.]]		[[Category: Lammens, A.]]
	[[Category: Lammens, K.]]		[[Category: Lammens, K.]]
-	[[Category: Alternative splicing]]
	[[Category: Antiviral defense]]		[[Category: Antiviral defense]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
Line 38:		Line 25:
	[[Category: Interferon induction]]		[[Category: Interferon induction]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
-	[[Category: Polymorphism]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
-	[[Category: Ubl conjugation]]
	[[Category: Zinc finger]]		[[Category: Zinc finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:37:10 2009''

OCA at 03:37, 17 February 2009

OCA — Tue, 17 Feb 2009 03:37:10 GMT

←Older revision		Revision as of 03:37, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2QFD is a ~~[[Single protein]]~~ 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=2QFD OCA].	+	2QFD is a 10 chains structure of sequences 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=2QFD OCA].

	==Reference==		==Reference==
-	The C-Terminal Regulatory Domain Is the RNA 5'-Triphosphate Sensor of RIG-I., Cui S, Eisenacher K, Kirchhofer A, Brzozka K, Lammens A, Lammens K, Fujita T, Conzelmann KK, Krug A, Hopfner KP, Mol Cell. 2008 Feb 1;29(2):169-179. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18243112 18243112]~~	+	<ref group="xtra">PMID:18243112</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Single protein]]
	[[Category: Cui, S.]]		[[Category: Cui, S.]]
	[[Category: Hopfner, K P.]]		[[Category: Hopfner, K P.]]
Line 44:		Line 43:
	[[Category: Zinc finger]]		[[Category: Zinc finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 09~~:00:~~36 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:37:10 2009''

OCA at 06:00, 28 July 2008

OCA — Mon, 28 Jul 2008 06:00:40 GMT

←Older revision		Revision as of 06:00, 28 July 2008
Line 1:		Line 1:
-	[[Image:2qfd.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2qfd.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2qfd\| PDB=2qfd \| SCENE= }}		{{STRUCTURE_2qfd\| PDB=2qfd \| SCENE= }}

-	~~'''~~Crystal structure of the regulatory domain of human RIG-I with bound Hg~~'''~~	+	===Crystal structure of the regulatory domain of human RIG-I with bound Hg===


-	~~==Overview==~~	+	<!--
-	The ~~ATPase RIG-I senses viral RNAs that contain 5'-triphosphates in the cytoplasm. It initiates a signaling cascade that activates innate immune response by interferon and cytokine production~~, ~~providing essential antiviral protection for~~ the ~~host. The mode of RNA 5'-triphosphate sensing by RIG-I remains elusive. We show that~~ the C-terminal regulatory domain RD of RIG-I binds viral RNA in a 5'-triphosphate-dependent manner and activates the RIG-I ATPase by RNA-dependent dimerization. The crystal structure of RD reveals a zinc-binding domain that is structurally related to GDP/~~GTP exchange factors of Rab-like GTPases~~. ~~The zinc coordination site~~ is ~~essential for RIG-I signaling and is also conserved in MDA5 and LGP2, suggesting related RD domains in all three enzymes~~. ~~Structure~~-~~guided mutagenesis identifies a positively charged groove as likely 5'~~-~~triphosphate-binding site of RIG-I. This groove is distinct in MDA5 and LGP2, raising the possibility that RD confers ligand specificity.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_18243112}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18243112 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18243112}}

	==About this Structure==		==About this Structure==
Line 39:		Line 43:
	[[Category: Ubl conjugation]]		[[Category: Ubl conjugation]]
	[[Category: Zinc finger]]		[[Category: Zinc finger]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 14~~:51:51 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:00:36 2008''