6o0w - Revision history

OCA at 14:50, 13 March 2024

OCA — Wed, 13 Mar 2024 14:50:09 GMT

←Older revision		Revision as of 14:50, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6o0w' size='340' side='right'caption='[[6o0w]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6o0w' size='340' side='right'caption='[[6o0w]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o0w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Muscadine_grape Muscadine grape~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O0W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O0W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o0w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vitis_rotundifolia Vitis rotundifolia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O0W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O0W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2P:ADENOSINE-2-5-DIPHOSPHATE'>A2P</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</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]] 1.75Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RUN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=103349 Muscadine grape])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2P:ADENOSINE-2-5-DIPHOSPHATE'>A2P</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</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=6o0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0w OCA], [~~http~~://pdbe.org/6o0w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o0w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o0w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0w 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=6o0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0w OCA], [https://pdbe.org/6o0w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o0w RCSB], [https://www.ebi.ac.uk/pdbsum/6o0w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RUN1_VITRO RUN1_VITRO]] Disease resistance (R) protein that confers resistance to multiple powdery and downy mildew by promoting cell death (PubMed:24033846, PubMed:31439792). Acts as a NAD(+) hydrolase (NADase): in response to activation, catalyzes cleavage of NAD(+) into ADP-D-ribose (ADPR) and nicotinamide; NAD(+) cleavage triggering a defense system that promotes cell death (PubMed:31439792). Also able to hydrolyze NADP(+), but not other NAD(+)-related molecules (PubMed:31439792).<ref>PMID:24033846</ref> <ref>PMID:31439792</ref>	+	[https://www.uniprot.org/uniprot/RUN1_VITRO RUN1_VITRO] Disease resistance (R) protein that confers resistance to multiple powdery and downy mildew by promoting cell death (PubMed:24033846, PubMed:31439792). Acts as a NAD(+) hydrolase (NADase): in response to activation, catalyzes cleavage of NAD(+) into ADP-D-ribose (ADPR) and nicotinamide; NAD(+) cleavage triggering a defense system that promotes cell death (PubMed:31439792). Also able to hydrolyze NADP(+), but not other NAD(+)-related molecules (PubMed:31439792).<ref>PMID:24033846</ref> <ref>PMID:31439792</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>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6o0w" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 15:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Muscadine grape~~]]	+	[[Category: Vitis rotundifolia]]
-	[[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: 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: ~~Plant disease resistance]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 11:45, 1 January 2020

OCA — Wed, 01 Jan 2020 11:45:54 GMT

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

-	~~The entry~~ 6o0w is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the TIR domain from the grapevine disease resistance protein RUN1 in complex with NADP+ and Bis-Tris==
		+	<StructureSection load='6o0w' size='340' side='right'caption='[[6o0w]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6o0w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Muscadine_grape Muscadine grape]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O0W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O0W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2P:ADENOSINE-2-5-DIPHOSPHATE'>A2P</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RUN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=103349 Muscadine grape])</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=6o0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o0w OCA], [http://pdbe.org/6o0w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o0w RCSB], [http://www.ebi.ac.uk/pdbsum/6o0w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o0w ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RUN1_VITRO RUN1_VITRO]] Disease resistance (R) protein that confers resistance to multiple powdery and downy mildew by promoting cell death (PubMed:24033846, PubMed:31439792). Acts as a NAD(+) hydrolase (NADase): in response to activation, catalyzes cleavage of NAD(+) into ADP-D-ribose (ADPR) and nicotinamide; NAD(+) cleavage triggering a defense system that promotes cell death (PubMed:31439792). Also able to hydrolyze NADP(+), but not other NAD(+)-related molecules (PubMed:31439792).<ref>PMID:24033846</ref> <ref>PMID:31439792</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:~~ Horsefield, S., Burdett, H., Zhang, X., Manik~~, M.K.~~, Shi, Y., Chen, J., ~~Tiancong, Q.~~, Gilley, J., Lai~~, J., Gu, W.~~, Rank~~, M.~~, Casey, L., Ericsson~~, D.J.~~, Foley, G., Hughes~~, R.O.~~, Bosanac, T., von Itzstein, M., Rathjen~~, J.P.~~, Nanson~~, J.D.~~, Boden, M., Dry~~, I.B.~~, Williams~~, S.J.~~, Staskawicz~~, B.J.~~, Coleman~~, M.P.~~, Ve, T., Dodds~~, P.N.~~, Kobe, B.	+	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: Crystal structure~~ of the ~~TIR domain from the grapevine disease resistance protein RUN1 in complex with NADP+ and Bis~~-~~Tris~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Kobe, B~~]]	+	<div class="pdbe-citations 6o0w" style="background-color:#fffaf0;"></div>
-	[[Category: Ve, T]]	+	== References ==
-	[[Category: ~~Ericsson~~, ~~D.J~~]]	+	<references/>
-	[[Category: ~~Chen~~, J]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Muscadine grape]]
		+	[[Category: Boden, M]]
		+	[[Category: Bosanac, T]]
		+	[[Category: Burdett, H]]
	[[Category: Casey, L]]		[[Category: Casey, L]]
-	[[Category: ~~Manik~~, M.K]]	+	[[Category: Chen, J]]
-	[[Category: ~~Nanson~~, J.D]]	+	[[Category: Coleman, M P]]
		+	[[Category: Dodds, P N]]
		+	[[Category: Dry, I B]]
		+	[[Category: Ericsson, D J]]
	[[Category: Foley, G]]		[[Category: Foley, G]]
-	[[Category: ~~Zhang, X]]~~	+	[[Category: Gilley, J]]
-	~~[[Category: Tiancong, Q]]~~	+	[[Category: Gu, W]]
-	~~[[Category: Lai~~, J]]	+
-	[[Category: ~~Williams~~, ~~S.J]]~~	+
-	~~[[Category: Dry, I.B]]~~	+
-	~~[[Category: Burdett, H]]~~	+
-	~~[[Category: Rathjen, J.P~~]]	+
	[[Category: Horsefield, S]]		[[Category: Horsefield, S]]
-	[[Category: ~~Dodds~~, ~~P.N~~]]	+	[[Category: Hughes, R O]]
-	[[Category: ~~Boden~~, M]]	+	[[Category: Itzstein, M von]]
-	[[Category: ~~Von Itzstein~~, M]]	+	[[Category: Kobe, B]]
-	[[Category: ~~Hughes~~, ~~R.O~~]]	+	[[Category: Lai, J]]
-	[[Category: ~~Coleman~~, M.P]]	+	[[Category: Manik, M K]]
-	[[Category: ~~Bosanac~~, T]]	+	[[Category: Nanson, J D]]
	[[Category: Rank, M]]		[[Category: Rank, M]]
-	[[Category: ~~Gu, W]]~~	+	[[Category: Rathjen, J P]]
-	~~[[Category: Gilley~~, J]]	+
	[[Category: Shi, Y]]		[[Category: Shi, Y]]
-	[[Category: Staskawicz, B.J]]	+	[[Category: Staskawicz, B J]]
		+	[[Category: Tiancong, Q]]
		+	[[Category: Ve, T]]
		+	[[Category: Williams, S J]]
		+	[[Category: Zhang, X]]
		+	[[Category: Plant disease resistance]]
		+	[[Category: Signaling protein]]

OCA at 04:57, 27 March 2019

OCA — Wed, 27 Mar 2019 04:57:24 GMT

←Older revision		Revision as of 04:57, 27 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o0w is ON HOLD	+	The entry 6o0w is ON HOLD until Paper Publication

	Authors: Horsefield, S., Burdett, H., Zhang, X., Manik, M.K., Shi, Y., Chen, J., Tiancong, Q., Gilley, J., Lai, J., Gu, W., Rank, M., Casey, L., Ericsson, D.J., Foley, G., Hughes, R.O., Bosanac, T., von Itzstein, M., Rathjen, J.P., Nanson, J.D., Boden, M., Dry, I.B., Williams, S.J., Staskawicz, B.J., Coleman, M.P., Ve, T., Dodds, P.N., Kobe, B.		Authors: Horsefield, S., Burdett, H., Zhang, X., Manik, M.K., Shi, Y., Chen, J., Tiancong, Q., Gilley, J., Lai, J., Gu, W., Rank, M., Casey, L., Ericsson, D.J., Foley, G., Hughes, R.O., Bosanac, T., von Itzstein, M., Rathjen, J.P., Nanson, J.D., Boden, M., Dry, I.B., Williams, S.J., Staskawicz, B.J., Coleman, M.P., Ve, T., Dodds, P.N., Kobe, B.

OCA: Protected "6o0w" [edit=sysop:move=sysop]

OCA — Wed, 27 Feb 2019 13:48:26 GMT

Protected "6o0w" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:48, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6o0w is ON HOLD Authors: Horsefield, S., Burdett, H., Zhang, X., Manik, M.K., Shi, Y., Chen, J., Tiancong, Q., Gilley, J., Lai, J., Gu, W., Rank, M....

OCA — Wed, 27 Feb 2019 13:48:24 GMT

New page: '''Unreleased structure''' The entry 6o0w is ON HOLD Authors: Horsefield, S., Burdett, H., Zhang, X., Manik, M.K., Shi, Y., Chen, J., Tiancong, Q., Gilley, J., Lai, J., Gu, W., Rank, M....

New page

'''Unreleased structure'''

The entry 6o0w is ON HOLD

Authors: Horsefield, S., Burdett, H., Zhang, X., Manik, M.K., Shi, Y., Chen, J., Tiancong, Q., Gilley, J., Lai, J., Gu, W., Rank, M., Casey, L., Ericsson, D.J., Foley, G., Hughes, R.O., Bosanac, T., von Itzstein, M., Rathjen, J.P., Nanson, J.D., Boden, M., Dry, I.B., Williams, S.J., Staskawicz, B.J., Coleman, M.P., Ve, T., Dodds, P.N., Kobe, B.

Description: Crystal structure of the TIR domain from the grapevine disease resistance protein RUN1 in complex with NADP+ and Bis-Tris
[[Category: Unreleased Structures]]
[[Category: Kobe, B]]
[[Category: Ve, T]]
[[Category: Ericsson, D.J]]
[[Category: Chen, J]]
[[Category: Casey, L]]
[[Category: Manik, M.K]]
[[Category: Nanson, J.D]]
[[Category: Foley, G]]
[[Category: Zhang, X]]
[[Category: Tiancong, Q]]
[[Category: Lai, J]]
[[Category: Williams, S.J]]
[[Category: Dry, I.B]]
[[Category: Burdett, H]]
[[Category: Rathjen, J.P]]
[[Category: Horsefield, S]]
[[Category: Dodds, P.N]]
[[Category: Boden, M]]
[[Category: Von Itzstein, M]]
[[Category: Hughes, R.O]]
[[Category: Coleman, M.P]]
[[Category: Bosanac, T]]
[[Category: Rank, M]]
[[Category: Gu, W]]
[[Category: Gilley, J]]
[[Category: Shi, Y]]
[[Category: Staskawicz, B.J]]