6o0q - Revision history

OCA at 14:49, 13 March 2024

OCA — Wed, 13 Mar 2024 14:49:44 GMT

←Older revision		Revision as of 14:49, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6o0q' size='340' side='right'caption='[[6o0q]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6o0q' size='340' side='right'caption='[[6o0q]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o0q]] is a 2 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=6O0Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O0Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o0q]] is a 2 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=6O0Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O0Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=BDR:BETA~~-~~D-RIBOFURANOSYL'>BDR</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SARM1, KIAA0524, SAMD2, SARM ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDR:BETA-D-RIBOFURANOSYL'>BDR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=6o0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0q OCA], [~~http~~://pdbe.org/6o0q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o0q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o0q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0q 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=6o0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0q OCA], [https://pdbe.org/6o0q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o0q RCSB], [https://www.ebi.ac.uk/pdbsum/6o0q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SARM1_HUMAN SARM1_HUMAN]] Negative regulator of MYD88- and TRIF-dependent toll-like receptor signaling pathway which plays a pivotal role in activating axonal degeneration following injury. Promotes Wallerian degeneration an injury-induced axonal death pathway which involves degeneration of an axon distal to the injury site. Can activate neuronal death in response to stress. Regulates dendritic arborization through the MAPK4-JNK pathway. Involved in innate immune response. Inhibits both TICAM1/TRIF- and MYD88-dependent activation of JUN/AP-1, TRIF-dependent activation of NF-kappa-B and IRF3, and the phosphorylation of MAPK14/p38.<ref>PMID:15123841</ref> <ref>PMID:16964262</ref> <ref>PMID:16985498</ref> <ref>PMID:20306472</ref>	+	[https://www.uniprot.org/uniprot/SARM1_HUMAN SARM1_HUMAN] Negative regulator of MYD88- and TRIF-dependent toll-like receptor signaling pathway which plays a pivotal role in activating axonal degeneration following injury. Promotes Wallerian degeneration an injury-induced axonal death pathway which involves degeneration of an axon distal to the injury site. Can activate neuronal death in response to stress. Regulates dendritic arborization through the MAPK4-JNK pathway. Involved in innate immune response. Inhibits both TICAM1/TRIF- and MYD88-dependent activation of JUN/AP-1, TRIF-dependent activation of NF-kappa-B and IRF3, and the phosphorylation of MAPK14/p38.<ref>PMID:15123841</ref> <ref>PMID:16964262</ref> <ref>PMID:16985498</ref> <ref>PMID:20306472</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD(+)) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection. Both processes depend on closely related Toll/interleukin-1 receptor (TIR) domains in these proteins, which, as we show, feature self-association-dependent NAD(+) cleavage activity associated with cell death signaling. We further show that SARM1 SAM (sterile alpha motif) domains form an octamer essential for axon degeneration that contributes to TIR domain enzymatic activity. The crystal structures of ribose and NADP(+) (the oxidized form of nicotinamide adenine dinucleotide phosphate) complexes of SARM1 and plant NLR RUN1 TIR domains, respectively, reveal a conserved substrate binding site. NAD(+) cleavage by TIR domains is therefore a conserved feature of animal and plant cell death signaling pathways.	+

-	NAD(+) cleavage activity by animal and plant TIR domains in cell death pathways.,Horsefield S, Burdett H, Zhang X, Manik MK, Shi Y, Chen J, Qi T, Gilley J, Lai JS, Rank MX, Casey LW, Gu W, Ericsson DJ, Foley G, Hughes RO, Bosanac T, von Itzstein M, Rathjen JP, Nanson JD, Boden M, Dry IB, Williams SJ, Staskawicz BJ, Coleman MP, Ve T, Dodds PN, Kobe B Science. 2019 Aug 23;365(6455):793-799. doi: 10.1126/science.aax1911. PMID:31439792<ref>PMID:31439792</ref>	+	==See Also==
-		+	*[[SARM1 3D structures\|SARM1 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6o0q" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boden, M]]	+	[[Category: Boden M]]
-	[[Category: Bosanac, T]]	+	[[Category: Bosanac T]]
-	[[Category: Burdett, H]]	+	[[Category: Burdett H]]
-	[[Category: Casey, L]]	+	[[Category: Casey L]]
-	[[Category: Chen, J]]	+	[[Category: Chen J]]
-	[[Category: Coleman~~, M P~~]]	+	[[Category: Coleman MP]]
-	[[Category: Deerain, N]]	+	[[Category: Deerain N]]
-	[[Category: Dodds~~, P N~~]]	+	[[Category: Dodds PN]]
-	[[Category: Dry~~, I B~~]]	+	[[Category: Dry IB]]
-	[[Category: Ericsson~~, D J~~]]	+	[[Category: Ericsson DJ]]
-	[[Category: Foley, G]]	+	[[Category: Foley G]]
-	[[Category: Gilley, J]]	+	[[Category: Gilley J]]
-	[[Category: Gu, W]]	+	[[Category: Gu W]]
-	[[Category: Horsefield, S]]	+	[[Category: Horsefield S]]
-	[[Category: Hughes~~, R O]]~~	+	[[Category: Hughes RO]]
-	~~[[Category: Itzstein, M von~~]]	+	[[Category: Kobe B]]
-	[[Category: Kobe, B]]	+	[[Category: Lai J]]
-	[[Category: Lai, J]]	+	[[Category: Manik MK]]
-	[[Category: Manik~~, M K~~]]	+	[[Category: Nanson JD]]
-	[[Category: Nanson~~, J D~~]]	+	[[Category: Rank M]]
-	[[Category: Rank, M]]	+	[[Category: Rathjen JP]]
-	[[Category: Rathjen~~, J P~~]]	+	[[Category: Shi Y]]
-	[[Category: Shi, Y]]	+	[[Category: Staskawicz BJ]]
-	[[Category: Staskawicz~~, B J~~]]	+	[[Category: Tiancong Q]]
-	[[Category: Tiancong, Q]]	+	[[Category: Ve T]]
-	[[Category: Ve, T]]	+	[[Category: Williams SJ]]
-	[[Category: Williams~~, S J~~]]	+	[[Category: Zhang X]]
-	[[Category: Zhang, X]]	+	[[Category: Von Itzstein M]]
-	[[Category: ~~Axon degeneration]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 11:45, 1 January 2020

OCA — Wed, 01 Jan 2020 11:45:00 GMT

←Older revision		Revision as of 11:45, 1 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6o0q is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the TIR domain from human SARM1 in complex with ribose==
		+	<StructureSection load='6o0q' size='340' side='right'caption='[[6o0q]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6o0q]] is a 2 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=6O0Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O0Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BDR:BETA-D-RIBOFURANOSYL'>BDR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SARM1, KIAA0524, SAMD2, SARM ([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=6o0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0q OCA], [http://pdbe.org/6o0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o0q RCSB], [http://www.ebi.ac.uk/pdbsum/6o0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0q ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SARM1_HUMAN SARM1_HUMAN]] Negative regulator of MYD88- and TRIF-dependent toll-like receptor signaling pathway which plays a pivotal role in activating axonal degeneration following injury. Promotes Wallerian degeneration an injury-induced axonal death pathway which involves degeneration of an axon distal to the injury site. Can activate neuronal death in response to stress. Regulates dendritic arborization through the MAPK4-JNK pathway. Involved in innate immune response. Inhibits both TICAM1/TRIF- and MYD88-dependent activation of JUN/AP-1, TRIF-dependent activation of NF-kappa-B and IRF3, and the phosphorylation of MAPK14/p38.<ref>PMID:15123841</ref> <ref>PMID:16964262</ref> <ref>PMID:16985498</ref> <ref>PMID:20306472</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD(+)) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection. Both processes depend on closely related Toll/interleukin-1 receptor (TIR) domains in these proteins, which, as we show, feature self-association-dependent NAD(+) cleavage activity associated with cell death signaling. We further show that SARM1 SAM (sterile alpha motif) domains form an octamer essential for axon degeneration that contributes to TIR domain enzymatic activity. The crystal structures of ribose and NADP(+) (the oxidized form of nicotinamide adenine dinucleotide phosphate) complexes of SARM1 and plant NLR RUN1 TIR domains, respectively, reveal a conserved substrate binding site. NAD(+) cleavage by TIR domains is therefore a conserved feature of animal and plant cell death signaling pathways.

-	~~Authors~~:	+	NAD(+) cleavage activity by animal and plant TIR domains in cell death pathways.,Horsefield S, Burdett H, Zhang X, Manik MK, Shi Y, Chen J, Qi T, Gilley J, Lai JS, Rank MX, Casey LW, Gu W, Ericsson DJ, Foley G, Hughes RO, Bosanac T, von Itzstein M, Rathjen JP, Nanson JD, Boden M, Dry IB, Williams SJ, Staskawicz BJ, Coleman MP, Ve T, Dodds PN, Kobe B Science. 2019 Aug 23;365(6455):793-799. doi: 10.1126/science.aax1911. PMID:31439792<ref>PMID:31439792</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6o0q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
		+	[[Category: Boden, M]]
		+	[[Category: Bosanac, T]]
		+	[[Category: Burdett, H]]
		+	[[Category: Casey, L]]
		+	[[Category: Chen, J]]
		+	[[Category: Coleman, M P]]
		+	[[Category: Deerain, N]]
		+	[[Category: Dodds, P N]]
		+	[[Category: Dry, I B]]
		+	[[Category: Ericsson, D J]]
		+	[[Category: Foley, G]]
		+	[[Category: Gilley, J]]
		+	[[Category: Gu, W]]
		+	[[Category: Horsefield, S]]
		+	[[Category: Hughes, R O]]
		+	[[Category: Itzstein, M von]]
		+	[[Category: Kobe, B]]
		+	[[Category: Lai, J]]
		+	[[Category: Manik, M K]]
		+	[[Category: Nanson, J D]]
		+	[[Category: Rank, M]]
		+	[[Category: Rathjen, J P]]
		+	[[Category: Shi, Y]]
		+	[[Category: Staskawicz, B J]]
		+	[[Category: Tiancong, Q]]
		+	[[Category: Ve, T]]
		+	[[Category: Williams, S J]]
		+	[[Category: Zhang, X]]
		+	[[Category: Axon degeneration]]
		+	[[Category: Signaling protein]]

OCA at 04:56, 27 March 2019

OCA — Wed, 27 Mar 2019 04:56:49 GMT

←Older revision		Revision as of 04:56, 27 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o0q is ON HOLD	+	The entry 6o0q is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6o0q" [edit=sysop:move=sysop]

OCA — Wed, 27 Feb 2019 13:46:59 GMT

Protected "6o0q" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:46, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6o0q is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Feb 2019 13:46:58 GMT

New page: '''Unreleased structure''' The entry 6o0q is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6o0q is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]