6j6p - Revision history

OCA at 10:02, 22 November 2023

OCA — Wed, 22 Nov 2023 10:02:14 GMT

←Older revision		Revision as of 10:02, 22 November 2023
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	<StructureSection load='6j6p' size='340' side='right'caption='[[6j6p]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='6j6p' size='340' side='right'caption='[[6j6p]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j6p]] is a 1 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=6J6P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6J6P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j6p]] is a 1 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=6J6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J6P 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 1.53Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RyR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=51655 Diamondback moth])~~</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=6j6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j6p OCA], [~~http~~://pdbe.org/6j6p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6j6p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6j6p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6j6p 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=6j6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j6p OCA], [https://pdbe.org/6j6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j6p RCSB], [https://www.ebi.ac.uk/pdbsum/6j6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j6p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I3NWV8_PLUXY I3NWV8_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 6j6p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6j6p" 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: ~~Xu, T~~]]	+	[[Category: Lin L]]
-	[[Category: ~~Yuchi, Z~~]]	+	[[Category: Xu T]]
-	[[Category: ~~Metal transport]]~~	+	[[Category: Yuchi Z]]
-	~~[[Category: Phosphorylation domain]]~~	+
-	~~[[Category: Ryanodine receptor]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 07:55, 23 October 2019

OCA — Wed, 23 Oct 2019 07:55:35 GMT

←Older revision		Revision as of 07:55, 23 October 2019
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	<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=6j6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j6p OCA], [http://pdbe.org/6j6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j6p RCSB], [http://www.ebi.ac.uk/pdbsum/6j6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j6p 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=6j6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j6p OCA], [http://pdbe.org/6j6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j6p RCSB], [http://www.ebi.ac.uk/pdbsum/6j6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j6p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Ryanodine receptor (RyR), a calcium-release channel located in the sarcoplasmic reticulum membrane of muscles, is the target of insecticides used against a wide range of agricultural pests. Mammalian RyRs have been shown to be under the regulatory control of several kinases and phosphatases, but little is known about the regulation of insect RyRs by phosphorylation. RESULTS: Here we present the crystal structures of wild-type and phospho-mimetic RyR Repeat34 domain containing PKA phosphorylation sites from diamondback moth (DBM), a major lepidopteran pest of cruciferous vegetables. The structure has unique features, not seen in mammalian RyRs, including an additional alpha-helix near the phosphorylation loop. Using tandem mass spectrometry, we identify several PKA sites clustering in the phosphorylation loop and the newly identified alpha-helix. Bioinformatics analysis shows that this alpha-helix is only present in Lepidoptera, suggesting an insect-specific regulation. Interestingly, the specific phosphorylation pattern is temperature-dependent. The thermal stability of the DBM Repeat34 domain is significantly lower than that of the analogous domain in the three mammalian RyR isoforms, indicating a more dynamic domain structure that can be partially unfolded to facilitate the temperature-dependent phosphorylation. Docking the structure into the cryo-electron microscopy model of full-length RyR reveals that the interface between the Repeat34 and neighboring HD1 domain is more conserved than that of the phosphorylation loop region that might be involved in the interaction with SPRY3 domain. We also identify an insect-specific glycerol-binding pocket that could be potentially targeted by novel insecticides to fight the current resistance crisis. CONCLUSIONS: The crystal structures of the DBM Repeat34 domain reveals insect-specific temperature-dependent phosphorylation sites that may regulate insect ryanodine receptor function. It also reveals insect-specific structural features and a potential ligand-binding site that could be targeted in an effort to develop green pesticides with high species-specificity.
		+
		+	Crystal structure of diamondback moth ryanodine receptor Repeat34 domain reveals insect-specific phosphorylation sites.,Xu T, Yuchi Z BMC Biol. 2019 Oct 9;17(1):77. doi: 10.1186/s12915-019-0698-5. PMID:31597572<ref>PMID:31597572</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6j6p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:18, 16 October 2019

OCA — Wed, 16 Oct 2019 07:18:38 GMT

←Older revision		Revision as of 07:18, 16 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6j6p is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of diamondback moth ryanodine receptor phosphorylation domain(2836-3050) mutant S2946D==
-		+	<StructureSection load='6j6p' size='340' side='right'caption='[[6j6p]], [[Resolution\|resolution]] 1.53Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6j6p]] is a 1 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=6J6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J6P FirstGlance]. <br>
-	~~Description~~:	+	</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RyR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=51655 Diamondback moth])</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=6j6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j6p OCA], [http://pdbe.org/6j6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j6p RCSB], [http://www.ebi.ac.uk/pdbsum/6j6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j6p ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Diamondback moth]]
		+	[[Category: Large Structures]]
		+	[[Category: Lin, L]]
		+	[[Category: Xu, T]]
		+	[[Category: Yuchi, Z]]
		+	[[Category: Metal transport]]
		+	[[Category: Phosphorylation domain]]
		+	[[Category: Ryanodine receptor]]
		+	[[Category: Transport protein]]

OCA at 07:13, 13 February 2019

OCA — Wed, 13 Feb 2019 07:13:22 GMT

←Older revision		Revision as of 07:13, 13 February 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6j6p is ON HOLD	+	The entry 6j6p is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6j6p" [edit=sysop:move=sysop]

OCA — Wed, 30 Jan 2019 06:09:53 GMT

Protected "6j6p" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:09, 30 January 2019

OCA: New page: '''Unreleased structure''' The entry 6j6p is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Jan 2019 06:09:52 GMT

New page: '''Unreleased structure''' The entry 6j6p is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6j6p is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]