6gkm - Revision history

OCA at 01:02, 11 April 2020

2020-04-11T01:02:20Z

←Older revision		Revision as of 01:02, 11 April 2020
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	<SX load='6gkm' size='340' side='right' viewer='molstar' caption='[[6gkm]], [[Resolution\|resolution]] 3.87Å' scene=''>		<SX load='6gkm' size='340' side='right' viewer='molstar' caption='[[6gkm]], [[Resolution\|resolution]] 3.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6gkm]] is a 3 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=6GKM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6GKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6gkm]] is a 3 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=6GKM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6GKM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6g19\|6g19]], [[6g1s\|6g1s]], [[6g1x\|6g1x]], [[6gjz\|6gjz]], [[6gkh\|6gkh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6g19\|6g19]], [[6g1s\|6g1s]], [[6g1x\|6g1x]], [[6gjz\|6gjz]], [[6gkh\|6gkh]]</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 ([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=6gkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gkm OCA], [http://pdbe.org/6gkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gkm RCSB], [http://www.ebi.ac.uk/pdbsum/6gkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gkm ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6gkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gkm OCA], [http://pdbe.org/6gkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gkm RCSB], [http://www.ebi.ac.uk/pdbsum/6gkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gkm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:31, 6 March 2020

2020-03-06T21:31:21Z

←Older revision		Revision as of 21:31, 6 March 2020
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	==CryoEM structure of the MDA5-dsRNA filament in complex with ATP (10 mM)==		==CryoEM structure of the MDA5-dsRNA filament in complex with ATP (10 mM)==
-	<~~StructureSection~~ load='6gkm' size='340' side='right' caption='[[6gkm]], [[Resolution\|resolution]] 3.87Å' scene=''>	+	<SX load='6gkm' size='340' side='right' viewer='molstar' caption='[[6gkm]], [[Resolution\|resolution]] 3.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6gkm]] is a 3 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=6GKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GKM FirstGlance]. <br>		<table><tr><td colspan='2'>[[6gkm]] is a 3 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=6GKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GKM FirstGlance]. <br>
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	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]

OCA at 21:03, 2 December 2018

2018-12-02T21:03:24Z

←Older revision		Revision as of 21:03, 2 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6gkm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==CryoEM structure of the MDA5-dsRNA filament in complex with ATP (10 mM)==
		+	<StructureSection load='6gkm' size='340' side='right' caption='[[6gkm]], [[Resolution\|resolution]] 3.87Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6gkm]] is a 3 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=6GKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GKM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6g19\|6g19]], [[6g1s\|6g1s]], [[6g1x\|6g1x]], [[6gjz\|6gjz]], [[6gkh\|6gkh]]</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='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=6gkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gkm OCA], [http://pdbe.org/6gkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gkm RCSB], [http://www.ebi.ac.uk/pdbsum/6gkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gkm ProSAT]</span></td></tr>
		+	</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;">
		+	== Publication Abstract from PubMed ==
		+	Double-stranded RNA (dsRNA) is a potent proinflammatory signature of viral infection. Long cytosolic dsRNA is recognized by MDA5. The cooperative assembly of MDA5 into helical filaments on dsRNA nucleates the assembly of a multiprotein type I interferon signaling platform. Here, we determined cryoelectron microscopy (cryo-EM) structures of MDA5-dsRNA filaments with different helical twists and bound nucleotide analogs at resolutions sufficient to build and refine atomic models. The structures identify the filament-forming interfaces, which encode the dsRNA binding cooperativity and length specificity of MDA5. The predominantly hydrophobic interface contacts confer flexibility, reflected in the variable helical twist within filaments. Mutation of filament-forming residues can result in loss or gain of signaling activity. Each MDA5 molecule spans 14 or 15 RNA base pairs, depending on the twist. Variations in twist also correlate with variations in the occupancy and type of nucleotide in the active site, providing insights on how ATP hydrolysis contributes to MDA5-dsRNA recognition.

-	~~Authors~~:	+	Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis.,Yu Q, Qu K, Modis Y Mol Cell. 2018 Nov 7. pii: S1097-2765(18)30844-X. doi:, 10.1016/j.molcel.2018.10.012. PMID:30449722<ref>PMID:30449722</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6gkm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
		+	[[Category: RNA helicase]]
		+	[[Category: Modis, Y]]
		+	[[Category: Qu, K]]
		+	[[Category: Yu, Q]]
		+	[[Category: Atpase]]
		+	[[Category: Helical filament]]
		+	[[Category: Immune system]]
		+	[[Category: Innate immune receptor]]
		+	[[Category: Protein-rna complex]]

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

2018-05-30T04:17:11Z

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

←Older revision

Revision as of 04:17, 30 May 2018

OCA: New page: '''Unreleased structure''' The entry 6gkm is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2018-05-30T04:17:10Z

New page: '''Unreleased structure''' The entry 6gkm is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6gkm is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]