5y9v - Revision history

OCA at 08:25, 22 November 2023

OCA — Wed, 22 Nov 2023 08:25:10 GMT

←Older revision		Revision as of 08:25, 22 November 2023
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	<StructureSection load='5y9v' size='340' side='right'caption='[[5y9v]], [[Resolution\|resolution]] 2.84Å' scene=''>		<StructureSection load='5y9v' size='340' side='right'caption='[[5y9v]], [[Resolution\|resolution]] 2.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y9v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Diamondback_moth Diamondback moth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plutella_xylostella Plutella xylostella]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y9V FirstGlance]. <br>
-	</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=GOL:GLYCEROL'>GOL</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]] 2.841Å</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=5y9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9v OCA], [~~http~~://pdbe.org/5y9v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y9v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y9v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9v ProSAT]</span></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=GOL:GLYCEROL'>GOL</scene></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=5y9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9v OCA], [https://pdbe.org/5y9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y9v RCSB], [https://www.ebi.ac.uk/pdbsum/5y9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G8EME3_PLUXY G8EME3_PLUXY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5y9v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y9v" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ryanodine receptor 3D structures\|Ryanodine receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Diamondback moth]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lin, L~~]]	+	[[Category: Plutella xylostella]]
-	[[Category: ~~Yuchi, Z~~]]	+	[[Category: Lin L]]
-	[[Category: ~~Ion channel]]~~	+	[[Category: Yuchi Z]]
-	~~[[Category: Ryanodine receptor]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 09:46, 9 September 2020

OCA — Wed, 09 Sep 2020 09:46:24 GMT

←Older revision		Revision as of 09:46, 9 September 2020
Line 1:		Line 1:

-	==Crystal ~~sturcture~~ of diamondback moth ryanodine receptor N-terminal domain==	+	==Crystal structure of diamondback moth ryanodine receptor N-terminal domain==
-	<StructureSection load='5y9v' size='340' side='right' caption='[[5y9v]], [[Resolution\|resolution]] 2.84Å' scene=''>	+	<StructureSection load='5y9v' size='340' side='right'caption='[[5y9v]], [[Resolution\|resolution]] 2.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y9v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y9v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Diamondback_moth Diamondback moth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y9V 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=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</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=GOL:GLYCEROL'>GOL</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=5y9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9v OCA], [http://pdbe.org/5y9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y9v RCSB], [http://www.ebi.ac.uk/pdbsum/5y9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9v 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=5y9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9v OCA], [http://pdbe.org/5y9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y9v RCSB], [http://www.ebi.ac.uk/pdbsum/5y9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5y9v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y9v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ryanodine receptor 3D structures\|Ryanodine receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Diamondback moth]]
		+	[[Category: Large Structures]]
	[[Category: Lin, L]]		[[Category: Lin, L]]
	[[Category: Yuchi, Z]]		[[Category: Yuchi, Z]]
-	[[Category: Diamondback moth]]
	[[Category: Ion channel]]		[[Category: Ion channel]]
	[[Category: Ryanodine receptor]]		[[Category: Ryanodine receptor]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 06:22, 20 December 2017

OCA — Wed, 20 Dec 2017 06:22:10 GMT

←Older revision		Revision as of 06:22, 20 December 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5y9v is ~~ON HOLD until Paper~~ Publication	+	==Crystal sturcture of diamondback moth ryanodine receptor N-terminal domain==
		+	<StructureSection load='5y9v' size='340' side='right' caption='[[5y9v]], [[Resolution\|resolution]] 2.84Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y9v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y9V 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=GOL:GLYCEROL'>GOL</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=5y9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9v OCA], [http://pdbe.org/5y9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y9v RCSB], [http://www.ebi.ac.uk/pdbsum/5y9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9v ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ryanodine receptors (RyRs) are large calcium-release channels located in sarcoplasmic reticulum membrane. They play a central role in excitation-contraction coupling of muscle cells. Three commercialized insecticides targeting pest RyRs generate worldwide sales over 2 billion U.S. dollars annually, but the structure of insect RyRs remains elusive, hindering our understanding of the mode of action of RyR-targeting insecticides and the development of insecticide resistance in pests. Here we present the crystal structure of RyR N-terminal domain (NTD) (residue 1-205) at 2.84 A resolution from the diamondback moth (DBM), Plutella xylostella, a destructive pest devouring cruciferous crops all over the world. Similar to its mammalian homolog, DBM RyR NTD consists of a beta-trefoil folding motif and a flanking alpha helix. Interestingly, two regions in NTD interacting with neighboring domains showed distinguished conformations in DBM relative to mammalian RyRs. Using homology modeling and molecular dynamics simulation, we created a structural model of the N-terminal three domains, showing two unique binding pockets that could be targeted by potential species-specific insecticides. Thermal melt experiment showed that the stability of DBM RyR NTD was higher than mammalian RyRs, probably due to a stable intra-domain disulfide bond observed in the crystal structure. Previously DBM NTD was shown to be one of the two critical regions to interact with insecticide flubendiamide, but isothermal titration calorimetry experiments negated DBM NTD alone as a major binding site for flubendiamide.

-	~~Authors: Lin~~, L., ~~Yuchi~~, Z.	+	Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites.,Lin L, Liu C, Qin J, Wang J, Dong S, Chen W, He W, Gao Q, You M, Yuchi Z Insect Biochem Mol Biol. 2017 Dec 2;92:73-83. doi: 10.1016/j.ibmb.2017.11.009. PMID:29191465<ref>PMID:29191465</ref>

-	~~Description: Crystal sturcture~~ of ~~diamondback moth ryanodine receptor N-terminal domain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Yuchi, Z]]~~	+	<div class="pdbe-citations 5y9v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Lin, L]]		[[Category: Lin, L]]
		+	[[Category: Yuchi, Z]]
		+	[[Category: Diamondback moth]]
		+	[[Category: Ion channel]]
		+	[[Category: Ryanodine receptor]]
		+	[[Category: Transport protein]]

OCA: Protected "5y9v" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:19:00 GMT

Protected "5y9v" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:19, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y9v is ON HOLD until Paper Publication Authors: Lin, L., Yuchi, Z. Description: Crystal sturcture of diamondback moth ryanodine receptor N-termina...

OCA — Wed, 27 Sep 2017 16:18:59 GMT

New page: '''Unreleased structure''' The entry 5y9v is ON HOLD until Paper Publication Authors: Lin, L., Yuchi, Z. Description: Crystal sturcture of diamondback moth ryanodine receptor N-termina...

New page

'''Unreleased structure'''

The entry 5y9v is ON HOLD until Paper Publication

Authors: Lin, L., Yuchi, Z.

Description: Crystal sturcture of diamondback moth ryanodine receptor N-terminal domain
[[Category: Unreleased Structures]]
[[Category: Yuchi, Z]]
[[Category: Lin, L]]