5ygv - Revision history

OCA at 08:29, 22 November 2023

2023-11-22T08:29:39Z

←Older revision		Revision as of 08:29, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist==		==Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist==
-	<StructureSection load='5ygv' size='340' side='right' caption='[[5ygv]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5ygv' size='340' side='right'caption='[[5ygv]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ygv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ygv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YGV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8V6:(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic+acid'>8V6</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]] 2.5Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8V6:(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic+acid'>8V6</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=5ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygv OCA], [~~http~~://pdbe.org/5ygv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ygv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ygv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygv 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=5ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygv OCA], [https://pdbe.org/5ygv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ygv RCSB], [https://www.ebi.ac.uk/pdbsum/5ygv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PYR1_ARATH PYR1_ARATH]] Receptor for abscisic acid (ABA) required for ABA-mediated responses such as stomatal closure and germination inhibition. Inhibits the activity of group-A protein phosphatases type 2C (PP2Cs) when activated by ABA.<ref>PMID:19624469</ref> <ref>PMID:19407142</ref> <ref>PMID:19769575</ref>	+	[https://www.uniprot.org/uniprot/PYR1_ARATH PYR1_ARATH] Receptor for abscisic acid (ABA) required for ABA-mediated responses such as stomatal closure and germination inhibition. Inhibits the activity of group-A protein phosphatases type 2C (PP2Cs) when activated by ABA.<ref>PMID:19624469</ref> <ref>PMID:19407142</ref> <ref>PMID:19769575</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ygv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ygv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Abscisic acid receptor 3D structures\|Abscisic acid receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
-	[[Category: Akiyama, T]]	+	[[Category: Large Structures]]
-	[[Category: Iba, K]]	+	[[Category: Akiyama T]]
-	[[Category: Mimura, N]]	+	[[Category: Iba K]]
-	[[Category: Monda, K]]	+	[[Category: Mimura N]]
-	[[Category: Ohnishi, T]]	+	[[Category: Monda K]]
-	[[Category: Okamoto, M]]	+	[[Category: Ohnishi T]]
-	[[Category: Sue, M]]	+	[[Category: Okamoto M]]
-	[[Category: Takeuchi, J]]	+	[[Category: Sue M]]
-	[[Category: Todoroki, Y]]	+	[[Category: Takeuchi J]]
-	[[Category: Yajima, S]]	+	[[Category: Todoroki Y]]
-	~~[[Category: Hormone receptor~~]]	+	[[Category: Yajima S]]

OCA at 05:50, 30 May 2018

2018-05-30T05:50:59Z

←Older revision		Revision as of 05:50, 30 May 2018
Line 3:		Line 3:
	<StructureSection load='5ygv' size='340' side='right' caption='[[5ygv]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5ygv' size='340' side='right' caption='[[5ygv]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ygv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ygv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8V6:(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic+acid'>8V6</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8V6:(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic+acid'>8V6</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=5ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygv OCA], [http://pdbe.org/5ygv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygv RCSB], [http://www.ebi.ac.uk/pdbsum/5ygv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygv 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=5ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygv OCA], [http://pdbe.org/5ygv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygv RCSB], [http://www.ebi.ac.uk/pdbsum/5ygv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygv ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]
	[[Category: Iba, K]]		[[Category: Iba, K]]

OCA at 05:41, 18 April 2018

2018-04-18T05:41:19Z

←Older revision		Revision as of 05:41, 18 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ygv is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist==
		+	<StructureSection load='5ygv' size='340' side='right' caption='[[5ygv]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ygv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8V6:(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic+acid'>8V6</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=5ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygv OCA], [http://pdbe.org/5ygv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygv RCSB], [http://www.ebi.ac.uk/pdbsum/5ygv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYR1_ARATH PYR1_ARATH]] Receptor for abscisic acid (ABA) required for ABA-mediated responses such as stomatal closure and germination inhibition. Inhibits the activity of group-A protein phosphatases type 2C (PP2Cs) when activated by ABA.<ref>PMID:19624469</ref> <ref>PMID:19407142</ref> <ref>PMID:19769575</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In Arabidopsis, signaling of the stress hormone abscisic acid (ABA) is mediated by PYR/PYL/RCAR receptors (PYLs), which bind to and inhibit group-A protein phosphatases 2C (PP2Cs), the negative regulators of ABA. X-ray structures of several PYL-ABA and PYL-ABA-PP2C complexes have revealed that a conserved tryptophan in PP2Cs is inserted into a small tunnel adjacent to the C4' of ABA in the PYL-ABA complex and plays a crucial role in the formation and stabilization of the PYL-ABA-PP2C complex. Here, 4'-modified ABA analogues were designed to prevent the insertion of the tryptophan into the tunnel adjacent to the C4' of ABA in these complexes. These analogues were predicted to block PYL-PP2C receptor interactions and thus block ABA signaling. To test this, 4'- O-phenylpropynyl ABA analogues were synthesized as novel PYL antagonists (PANs). Structural, thermodynamic, biochemical, and physiological studies demonstrated that PANs completely abolished ABA-induced PYL-PP2C interactions in vitro and suppressed stress-induced ABA responses in vivo more strongly than did 3'-hexylsulfanyl-ABA (AS6), a PYL antagonist we developed previously. The PANs and AS6 antagonized the effects of ABA to different degrees in different plants, suggesting that these PANs can function as chemical scalpels to dissect the complicated regulatory mechanism of ABA signaling in plants.

-	~~Authors: Akiyama, T., Sue, M~~., Takeuchi, J., Mimura, N., Okamoto, M., Monda, K., Iba, K., Ohnishi, T., Todoroki, Y.~~, Yajima, S~~.	+	Structure-Based Chemical Design of Abscisic Acid Antagonists That Block PYL-PP2C Receptor Interactions.,Takeuchi J, Mimura N, Okamoto M, Yajima S, Sue M, Akiyama T, Monda K, Iba K, Ohnishi T, Todoroki Y ACS Chem Biol. 2018 Apr 11. doi: 10.1021/acschembio.8b00105. PMID:29620349<ref>PMID:29620349</ref>

-	~~Description: Crystal structure~~ of the ~~abscisic acid receptor PYR1 in complex with an antagonist~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Mimura, N]]~~	+	<div class="pdbe-citations 5ygv" style="background-color:#fffaf0;"></div>
-	~~[[Category: Takeuchi, J]]~~	+	== References ==
-	~~[[Category: Sue, M]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]
-	[[Category: Okamoto, M]]
	[[Category: Iba, K]]		[[Category: Iba, K]]
		+	[[Category: Mimura, N]]
		+	[[Category: Monda, K]]
	[[Category: Ohnishi, T]]		[[Category: Ohnishi, T]]
		+	[[Category: Okamoto, M]]
		+	[[Category: Sue, M]]
		+	[[Category: Takeuchi, J]]
	[[Category: Todoroki, Y]]		[[Category: Todoroki, Y]]
-	[[Category: Monda, K]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]
		+	[[Category: Hormone receptor]]

OCA at 06:23, 22 November 2017

2017-11-22T06:23:39Z

←Older revision		Revision as of 06:23, 22 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ygv is ON HOLD	+	The entry 5ygv is ON HOLD until Paper Publication

	Authors: Akiyama, T., Sue, M., Takeuchi, J., Mimura, N., Okamoto, M., Monda, K., Iba, K., Ohnishi, T., Todoroki, Y., Yajima, S.		Authors: Akiyama, T., Sue, M., Takeuchi, J., Mimura, N., Okamoto, M., Monda, K., Iba, K., Ohnishi, T., Todoroki, Y., Yajima, S.
Line 10:		Line 10:
	[[Category: Takeuchi, J]]		[[Category: Takeuchi, J]]
	[[Category: Sue, M]]		[[Category: Sue, M]]
-	[[Category: Okamoto, M]]
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]
-	[[Category: ~~Ohnishi~~, T]]	+	[[Category: Okamoto, M]]
	[[Category: Iba, K]]		[[Category: Iba, K]]
		+	[[Category: Ohnishi, T]]
	[[Category: Todoroki, Y]]		[[Category: Todoroki, Y]]
	[[Category: Monda, K]]		[[Category: Monda, K]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]

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

2017-10-04T08:04:33Z

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

←Older revision

Revision as of 08:04, 4 October 2017

OCA: New page: '''Unreleased structure''' The entry 5ygv is ON HOLD Authors: Akiyama, T., Sue, M., Takeuchi, J., Mimura, N., Okamoto, M., Monda, K., Iba, K., Ohnishi, T., Todoroki, Y., Yajima, S. Des...

2017-10-04T08:04:32Z

New page: '''Unreleased structure''' The entry 5ygv is ON HOLD Authors: Akiyama, T., Sue, M., Takeuchi, J., Mimura, N., Okamoto, M., Monda, K., Iba, K., Ohnishi, T., Todoroki, Y., Yajima, S. Des...

New page

'''Unreleased structure'''

The entry 5ygv is ON HOLD

Authors: Akiyama, T., Sue, M., Takeuchi, J., Mimura, N., Okamoto, M., Monda, K., Iba, K., Ohnishi, T., Todoroki, Y., Yajima, S.

Description: Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist
[[Category: Unreleased Structures]]
[[Category: Mimura, N]]
[[Category: Takeuchi, J]]
[[Category: Sue, M]]
[[Category: Okamoto, M]]
[[Category: Akiyama, T]]
[[Category: Ohnishi, T]]
[[Category: Iba, K]]
[[Category: Todoroki, Y]]
[[Category: Monda, K]]
[[Category: Yajima, S]]