5fhm - Revision history

OCA at 06:51, 19 July 2023

OCA — Wed, 19 Jul 2023 06:51:30 GMT

←Older revision		Revision as of 06:51, 19 July 2023
Line 1:		Line 1:

	==Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-(aminomethyl)benzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at resolution 1.55 A resolution==		==Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-(aminomethyl)benzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at resolution 1.55 A resolution==
-	<StructureSection load='5fhm' size='340' side='right' caption='[[5fhm]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5fhm' size='340' side='right'caption='[[5fhm]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fhm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fhm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FHM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XP:(2~{S})-3-[5-[2-[[3-(AMINOMETHYL)PHENYL]METHYL]-1,2,3,4-TETRAZOL-5-YL]-3-OXIDANYL-1,2-OXAZOL-4-YL]-2-AZANYL-PROPANOIC+ACID'>5XP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.55Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p2a\|2p2a]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5XP:(2~{S})-3-[5-[2-[[3-(AMINOMETHYL)PHENYL]METHYL]-1,2,3,4-TETRAZOL-5-YL]-3-OXIDANYL-1,2-OXAZOL-4-YL]-2-AZANYL-PROPANOIC+ACID'>5XP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Gria2, Glur2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</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=5fhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhm OCA], [https://pdbe.org/5fhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fhm RCSB], [https://www.ebi.ac.uk/pdbsum/5fhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhm 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=5fhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhm OCA], [~~http~~://pdbe.org/5fhm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fhm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fhm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GRIA2_RAT GRIA2_RAT]] Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate.<ref>PMID:9351977</ref> <ref>PMID:19265014</ref> <ref>PMID:21172611</ref> <ref>PMID:12501192</ref> <ref>PMID:12015593</ref> <ref>PMID:12872125</ref> <ref>PMID:12730367</ref> <ref>PMID:16192394</ref> <ref>PMID:15591246</ref> <ref>PMID:17018279</ref> <ref>PMID:16483599</ref> <ref>PMID:19946266</ref> <ref>PMID:21317873</ref> <ref>PMID:21846932</ref>	+	[https://www.uniprot.org/uniprot/GRIA2_RAT GRIA2_RAT] Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate.<ref>PMID:9351977</ref> <ref>PMID:19265014</ref> <ref>PMID:21172611</ref> <ref>PMID:12501192</ref> <ref>PMID:12015593</ref> <ref>PMID:12872125</ref> <ref>PMID:12730367</ref> <ref>PMID:16192394</ref> <ref>PMID:15591246</ref> <ref>PMID:17018279</ref> <ref>PMID:16483599</ref> <ref>PMID:19946266</ref> <ref>PMID:21317873</ref> <ref>PMID:21846932</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5fhm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fhm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamate receptor 3D structures\|Glutamate receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Large Structures]]
-	[[Category: Al-musaed, A]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Frydenvang, K]]	+	[[Category: Al-musaed A]]
-	[[Category: Kastrup~~, J S]]~~	+	[[Category: Frydenvang K]]
-	~~[[Category: Ionotropic glutamate receptor glua2]]~~	+	[[Category: Kastrup JS]]
-	~~[[Category: Ligand-binding domain]]~~	+
-	~~[[Category: Membrane protein~~]]	+

OCA at 08:05, 17 January 2018

OCA — Wed, 17 Jan 2018 08:05:02 GMT

←Older revision		Revision as of 08:05, 17 January 2018
Line 3:		Line 3:
	<StructureSection load='5fhm' size='340' side='right' caption='[[5fhm]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5fhm' size='340' side='right' caption='[[5fhm]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fhm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fhm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FHM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XP:(2~{S})-3-[5-[2-[[3-(AMINOMETHYL)PHENYL]METHYL]-1,2,3,4-TETRAZOL-5-YL]-3-OXIDANYL-1,2-OXAZOL-4-YL]-2-AZANYL-PROPANOIC+ACID'>5XP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XP:(2~{S})-3-[5-[2-[[3-(AMINOMETHYL)PHENYL]METHYL]-1,2,3,4-TETRAZOL-5-YL]-3-OXIDANYL-1,2-OXAZOL-4-YL]-2-AZANYL-PROPANOIC+ACID'>5XP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p2a\|2p2a]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p2a\|2p2a]]</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=5fhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhm OCA], [http://pdbe.org/5fhm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhm RCSB], [http://www.ebi.ac.uk/pdbsum/5fhm PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Gria2, Glur2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=5fhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhm OCA], [http://pdbe.org/5fhm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhm RCSB], [http://www.ebi.ac.uk/pdbsum/5fhm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Al-musaed, A]]		[[Category: Al-musaed, A]]
	[[Category: Frydenvang, K]]		[[Category: Frydenvang, K]]

OCA at 15:05, 2 March 2016

OCA — Wed, 02 Mar 2016 15:05:14 GMT

←Older revision		Revision as of 15:05, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fhm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-(aminomethyl)benzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at resolution 1.55 A resolution==
		+	<StructureSection load='5fhm' size='340' side='right' caption='[[5fhm]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fhm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FHM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XP:(2~{S})-3-[5-[2-[[3-(AMINOMETHYL)PHENYL]METHYL]-1,2,3,4-TETRAZOL-5-YL]-3-OXIDANYL-1,2-OXAZOL-4-YL]-2-AZANYL-PROPANOIC+ACID'>5XP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p2a\|2p2a]]</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=5fhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhm OCA], [http://pdbe.org/5fhm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhm RCSB], [http://www.ebi.ac.uk/pdbsum/5fhm PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GRIA2_RAT GRIA2_RAT]] Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate.<ref>PMID:9351977</ref> <ref>PMID:19265014</ref> <ref>PMID:21172611</ref> <ref>PMID:12501192</ref> <ref>PMID:12015593</ref> <ref>PMID:12872125</ref> <ref>PMID:12730367</ref> <ref>PMID:16192394</ref> <ref>PMID:15591246</ref> <ref>PMID:17018279</ref> <ref>PMID:16483599</ref> <ref>PMID:19946266</ref> <ref>PMID:21317873</ref> <ref>PMID:21846932</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A series of analogues of the (S)-2-Amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propionic acid (AMPA) receptor agonist BnTetAMPA (5b) were synthesized and characterized pharmacologically in radioligand binding assays at native and cloned AMPA receptors and functionally by two-electrode voltage clamp electrophysiology at the four homomeric AMPA receptors expressed in Xenopus laevis oocytes. The analogues 6 and 7 exhibit very different pharmacological profiles with binding affinity preference for the subtypes GluA1 and GluA3, respectively. X-ray crystal structures of three ligands (6, 7, and 8) in complex with the agonist binding domain (ABD) of GluA2 show that they induce full domain closure despite their low agonist efficacies. Trp767 in GluA2 ABD could be an important determinant for partial agonism of this compound series at AMPA receptors, since agonist efficacy also correlated with the location of the Trp767 side chain.

-	~~Authors: Kastrup, J.~~S., ~~Frydenvang~~, K., Al-~~musaed,~~ A.	+	Tweaking Subtype Selectivity and Agonist Efficacy at (S)-2-Amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propionic acid (AMPA) Receptors in a Small Series of BnTetAMPA Analogues.,Wang SY, Larsen Y, Navarrete CV, Jensen AA, Nielsen B, Al-Musaed A, Frydenvang K, Kastrup JS, Pickering DS, Clausen RP J Med Chem. 2016 Feb 22. PMID:26862980<ref>PMID:26862980</ref>

-	~~Description: Crystal structure~~ of the ~~GluA2 ligand-binding domain (S1S2J) in complex with (~~S)-2-~~Amino-3-(5-(2-(3-(aminomethyl)benzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at resolution 1.55 A resolution~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	[[Category: Al-~~Musaed~~, A]]	+	<div class="pdbe-citations 5fhm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Al-musaed, A]]
	[[Category: Frydenvang, K]]		[[Category: Frydenvang, K]]
-	[[Category: Kastrup, J.S]]	+	[[Category: Kastrup, J S]]
		+	[[Category: Ionotropic glutamate receptor glua2]]
		+	[[Category: Ligand-binding domain]]
		+	[[Category: Membrane protein]]

OCA at 23:59, 27 January 2016

OCA — Wed, 27 Jan 2016 23:59:56 GMT

←Older revision		Revision as of 23:59, 27 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kastrup, J.S., Frydenvang, K., Al-musaed, A.		Authors: Kastrup, J.S., Frydenvang, K., Al-musaed, A.

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

OCA — Wed, 30 Dec 2015 17:58:15 GMT

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

←Older revision

Revision as of 17:58, 30 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fhm is ON HOLD Authors: Kastrup, J.S., Frydenvang, K., Al-musaed, A. Description: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in ...

OCA — Wed, 30 Dec 2015 17:58:14 GMT

New page: '''Unreleased structure''' The entry 5fhm is ON HOLD Authors: Kastrup, J.S., Frydenvang, K., Al-musaed, A. Description: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in ...

New page

'''Unreleased structure'''

The entry 5fhm is ON HOLD

Authors: Kastrup, J.S., Frydenvang, K., Al-musaed, A.

Description: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-(aminomethyl)benzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at resolution 1.55 A resolution
[[Category: Unreleased Structures]]
[[Category: Al-Musaed, A]]
[[Category: Frydenvang, K]]
[[Category: Kastrup, J.S]]