5x2m - Revision history

OCA at 07:53, 22 November 2023

OCA — Wed, 22 Nov 2023 07:53:15 GMT

←Older revision		Revision as of 07:53, 22 November 2023
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	<StructureSection load='5x2m' size='340' side='right'caption='[[5x2m]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='5x2m' size='340' side='right'caption='[[5x2m]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x2m]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Japanese_killifish Japanese killifish~~] and [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X2M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x2m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Oryzias_latipes Oryzias latipes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X2M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.206Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2n\|5x2n]], [[5x2o\|5x2o]], [[5x2p\|5x2p]], [[5x2q\|5x2q]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TAS1R2a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8090 Japanese killifish]), TAS1R3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8090 Japanese killifish])</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=5x2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2m OCA], [https://pdbe.org/5x2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x2m RCSB], [https://www.ebi.ac.uk/pdbsum/5x2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2m 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=5x2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2m OCA], [~~http~~://pdbe.org/5x2m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x2m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x2m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2m ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A173M0G2_ORYLA A0A173M0G2_ORYLA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Japanese killifish]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Atsumi, N~~]]	+	[[Category: Oryzias latipes]]
-	[[Category: ~~Nuemket,~~ N]]	+	[[Category: Atsumi N]]
-	[[Category: ~~Yamashita, A]]~~	+	[[Category: Nuemket N]]
-	~~[[Category: Yasui,~~ N]]	+	[[Category: Yamashita A]]
-	[[Category: ~~Amino acid~~]]	+	[[Category: Yasui N]]
-	[[Category: ~~Ligand binding]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Signaling protein-immune system complex]]~~	+
-	~~[[Category: Venus-flytrap domain~~]]	+

OCA at 07:23, 7 October 2020

OCA — Wed, 07 Oct 2020 07:23:04 GMT

←Older revision		Revision as of 07:23, 7 October 2020
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	==Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine==		==Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine==
-	<StructureSection load='5x2m' size='340' side='right' caption='[[5x2m]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='5x2m' size='340' side='right'caption='[[5x2m]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x2m]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2M OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X2M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x2m]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_killifish Japanese killifish] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X2M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2n\|5x2n]], [[5x2o\|5x2o]], [[5x2p\|5x2p]], [[5x2q\|5x2q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2n\|5x2n]], [[5x2o\|5x2o]], [[5x2p\|5x2p]], [[5x2q\|5x2q]]</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=5x2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2m OCA], [http://pdbe.org/5x2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2m RCSB], [http://www.ebi.ac.uk/pdbsum/5x2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2m ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TAS1R2a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8090 Japanese killifish]), TAS1R3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8090 Japanese killifish])</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=5x2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2m OCA], [http://pdbe.org/5x2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2m RCSB], [http://www.ebi.ac.uk/pdbsum/5x2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2m ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Japanese killifish]]
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Atsumi, N]]		[[Category: Atsumi, N]]
	[[Category: Nuemket, N]]		[[Category: Nuemket, N]]

OCA at 09:59, 3 August 2017

OCA — Thu, 03 Aug 2017 09:59:52 GMT

←Older revision		Revision as of 09:59, 3 August 2017
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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=5x2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2m OCA], [http://pdbe.org/5x2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2m RCSB], [http://www.ebi.ac.uk/pdbsum/5x2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2m 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=5x2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2m OCA], [http://pdbe.org/5x2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2m RCSB], [http://www.ebi.ac.uk/pdbsum/5x2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2m ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The taste receptor type 1 (T1r) family perceives 'palatable' tastes. These receptors function as T1r2-T1r3 and T1r1-T1r3 heterodimers to recognize a wide array of sweet and umami (savory) tastes in sugars and amino acids. Nonetheless, it is unclear how diverse tastes are recognized by so few receptors. Here we present crystal structures of the extracellular ligand-binding domains (LBDs), the taste recognition regions of the fish T1r2-T1r3 heterodimer, bound to different amino acids. The ligand-binding pocket in T1r2LBD is rich in aromatic residues, spacious and accommodates hydrated percepts. Biophysical studies show that this binding site is characterized by a broad yet discriminating chemical recognition, contributing for the particular trait of taste perception. In contrast, the analogous pocket in T1r3LBD is occupied by a rather loosely bound amino acid, suggesting that the T1r3 has an auxiliary role. Overall, we provide a structural basis for understanding the chemical perception of taste receptors.
		+
		+	Structural basis for perception of diverse chemical substances by T1r taste receptors.,Nuemket N, Yasui N, Kusakabe Y, Nomura Y, Atsumi N, Akiyama S, Nango E, Kato Y, Kaneko MK, Takagi J, Hosotani M, Yamashita A Nat Commun. 2017 May 23;8:15530. doi: 10.1038/ncomms15530. PMID:28534491<ref>PMID:28534491</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x2m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:53, 24 May 2017

OCA — Wed, 24 May 2017 13:53:21 GMT

←Older revision		Revision as of 13:53, 24 May 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5x2m ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine==
-		+	<StructureSection load='5x2m' size='340' side='right' caption='[[5x2m]], [[Resolution\|resolution]] 2.21Å' scene=''>
-	~~Authors~~: ~~Nuemket, N~~., ~~Yasui~~, N., ~~Atsumi~~, N., ~~Yamashita~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x2m]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X2M FirstGlance]. <br>
-	~~Description~~: ~~Ligand binding domain of receptor~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2n\|5x2n]], [[5x2o\|5x2o]], [[5x2p\|5x2p]], [[5x2q\|5x2q]]</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=5x2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2m OCA], [http://pdbe.org/5x2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2m RCSB], [http://www.ebi.ac.uk/pdbsum/5x2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2m ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Atsumi, N]]		[[Category: Atsumi, N]]
		+	[[Category: Nuemket, N]]
		+	[[Category: Yamashita, A]]
	[[Category: Yasui, N]]		[[Category: Yasui, N]]
-	[[Category: ~~Yamashita, A~~]]	+	[[Category: Amino acid]]
-	[[Category: ~~Nuemket, N~~]]	+	[[Category: Ligand binding]]
		+	[[Category: Receptor]]
		+	[[Category: Signaling protein-immune system complex]]
		+	[[Category: Venus-flytrap domain]]

OCA at 20:07, 15 March 2017

OCA — Wed, 15 Mar 2017 20:07:06 GMT

←Older revision		Revision as of 20:07, 15 March 2017
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	Description: Ligand binding domain of receptor		Description: Ligand binding domain of receptor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Nuemket, N]]
	[[Category: Atsumi, N]]		[[Category: Atsumi, N]]
	[[Category: Yasui, N]]		[[Category: Yasui, N]]
	[[Category: Yamashita, A]]		[[Category: Yamashita, A]]
		+	[[Category: Nuemket, N]]

OCA: Protected "5x2m" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:37:13 GMT

Protected "5x2m" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:37, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x2m is ON HOLD until Paper Publication Authors: Nuemket, N., Yasui, N., Atsumi, N., Yamashita, A. Description: Ligand binding domain of receptor [...

OCA — Thu, 09 Mar 2017 15:37:12 GMT

New page: '''Unreleased structure''' The entry 5x2m is ON HOLD until Paper Publication Authors: Nuemket, N., Yasui, N., Atsumi, N., Yamashita, A. Description: Ligand binding domain of receptor [...

New page

'''Unreleased structure'''

The entry 5x2m is ON HOLD until Paper Publication

Authors: Nuemket, N., Yasui, N., Atsumi, N., Yamashita, A.

Description: Ligand binding domain of receptor
[[Category: Unreleased Structures]]
[[Category: Nuemket, N]]
[[Category: Atsumi, N]]
[[Category: Yasui, N]]
[[Category: Yamashita, A]]