6r8m - Revision history

OCA at 12:17, 24 January 2024

2024-01-24T12:17:12Z

←Older revision		Revision as of 12:17, 24 January 2024
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	<StructureSection load='6r8m' size='340' side='right'caption='[[6r8m]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6r8m' size='340' side='right'caption='[[6r8m]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r8m]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpi_841383_[[magnaporthe_oryzae]] Bpi 841383 [[magnaporthe oryzae]]~~] and [~~http~~://en.wikipedia.org/wiki/~~Orysa Orysa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R8M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R8M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r8m]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa] and [https://en.wikipedia.org/wiki/Pyricularia_oryzae Pyricularia oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R8M FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'~~>~~CL</scene>, <scene name='pdbligand=MPD:(4S)~~-~~2-METHYL-2~~,~~4-PENTANEDIOL'>MPD</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]] 1.85Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Pi-km1, Pikh-1 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=4530 ORYSA]~~), ~~AVR~~-~~Pik ([http:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318829 BPI 841383 [[Magnaporthe oryzae]]])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6r8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r8m OCA], [~~http~~://pdbe.org/6r8m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r8m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r8m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r8m 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=6r8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r8m OCA], [https://pdbe.org/6r8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r8m RCSB], [https://www.ebi.ac.uk/pdbsum/6r8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r8m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D5L9G5_ORYSJ D5L9G5_ORYSJ]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant nucleotide binding, leucine-rich repeat (NLR) receptors detect pathogen effectors and initiate an immune response. Since their discovery, NLRs have been the focus of protein engineering to improve disease resistance. However, this approach has proven challenging, in part due to their narrow response specificity. Previously, we revealed the structural basis of pathogen recognition by the integrated heavy metal associated (HMA) domain of the rice NLR Pikp (Maqbool et al., 2015). Here, we used structure-guided engineering to expand the response profile of Pikp to variants of the rice blast pathogen effector AVR-Pik. A mutation located within an effector-binding interface of the integrated Pikp-HMA domain increased the binding affinity for AVR-Pik variants in vitro and in vivo. This translates to an expanded cell-death response to AVR-Pik variants previously unrecognized by Pikp in planta. The structures of the engineered Pikp-HMA in complex with AVR-Pik variants revealed the mechanism of expanded recognition. These results provide a proof-of-concept that protein engineering can improve the utility of plant NLR receptors where direct interaction between effectors and NLRs is established, particularly where this interaction occurs via integrated domains.
		+
		+	Protein engineering expands the effector recognition profile of a rice NLR immune receptor.,De la Concepcion JC, Franceschetti M, MacLean D, Terauchi R, Kamoun S, Banfield MJ Elife. 2019 Sep 19;8:e47713. doi: 10.7554/eLife.47713. PMID:31535976<ref>PMID:31535976</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6r8m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Orysa~~]]	+	[[Category: Oryza sativa]]
-	[[Category: ~~Banfield, M J~~]]	+	[[Category: Pyricularia oryzae]]
-	[[Category: ~~Concepcion, J C.De la~~]]	+	[[Category: Banfield MJ]]
-	[[Category: ~~Franceschetti, M~~]]	+	[[Category: De la Concepcion JC]]
-	[[Category: ~~Complex]]~~	+	[[Category: Franceschetti M]]
-	~~[[Category: Hma]]~~	+
-	~~[[Category: Nlr]]~~	+
-	~~[[Category: Plant protein]]~~	+
-	~~[[Category: Rice blast~~]]	+

OCA at 06:41, 10 July 2019

2019-07-10T06:41:17Z

←Older revision		Revision as of 06:41, 10 July 2019
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	<StructureSection load='6r8m' size='340' side='right'caption='[[6r8m]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6r8m' size='340' side='right'caption='[[6r8m]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r8m]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R8M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r8m]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpi_841383_[[magnaporthe_oryzae]] Bpi 841383 [[magnaporthe oryzae]]] and [http://en.wikipedia.org/wiki/Orysa Orysa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R8M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pi-km1, Pikh-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4530 ORYSA]), AVR-Pik ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318829 BPI 841383 [[Magnaporthe oryzae]]])</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=6r8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r8m OCA], [http://pdbe.org/6r8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r8m RCSB], [http://www.ebi.ac.uk/pdbsum/6r8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r8m ProSAT]</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=6r8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r8m OCA], [http://pdbe.org/6r8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r8m RCSB], [http://www.ebi.ac.uk/pdbsum/6r8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r8m ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Orysa]]
	[[Category: Banfield, M J]]		[[Category: Banfield, M J]]
	[[Category: Concepcion, J C.De la]]		[[Category: Concepcion, J C.De la]]

OCA at 07:15, 24 April 2019

2019-04-24T07:15:32Z

←Older revision		Revision as of 07:15, 24 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6r8m is ON HOLD~~	+	==Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)==
-		+	<StructureSection load='6r8m' size='340' side='right'caption='[[6r8m]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~Authors: De la Concepcion, J.C., Franceschetti, M., Banfield, M.J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6r8m]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R8M FirstGlance]. <br>
-	~~Description:~~ Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6r8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r8m OCA], [http://pdbe.org/6r8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r8m RCSB], [http://www.ebi.ac.uk/pdbsum/6r8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r8m ProSAT]</span></td></tr>
-	[[Category: ~~De La Concepcion~~, J.C]]	+	</table>
-	[[Category: ~~Banfield~~, M.J]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Banfield, M J]]
		+	[[Category: Concepcion, J C.De la]]
	[[Category: Franceschetti, M]]		[[Category: Franceschetti, M]]
		+	[[Category: Complex]]
		+	[[Category: Hma]]
		+	[[Category: Nlr]]
		+	[[Category: Plant protein]]
		+	[[Category: Rice blast]]

OCA: Protected "6r8m" [edit=sysop:move=sysop]

2019-04-10T05:43:45Z

Protected "6r8m" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:43, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r8m is ON HOLD Authors: De la Concepcion, J.C., Franceschetti, M., Banfield, M.J. Description: Complex of rice blast (Magnaporthe oryzae) effector...

2019-04-10T05:43:43Z

New page: '''Unreleased structure''' The entry 6r8m is ON HOLD Authors: De la Concepcion, J.C., Franceschetti, M., Banfield, M.J. Description: Complex of rice blast (Magnaporthe oryzae) effector...

New page

'''Unreleased structure'''

The entry 6r8m is ON HOLD

Authors: De la Concepcion, J.C., Franceschetti, M., Banfield, M.J.

Description: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)
[[Category: Unreleased Structures]]
[[Category: De La Concepcion, J.C]]
[[Category: Banfield, M.J]]
[[Category: Franceschetti, M]]