5cmc - Revision history

OCA at 08:39, 27 September 2023

OCA — Wed, 27 Sep 2023 08:39:09 GMT

←Older revision		Revision as of 08:39, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cmc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mnemiopsis_leidyi Mnemiopsis leidyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CMC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cmc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mnemiopsis_leidyi Mnemiopsis leidyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CMC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.28Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [https://pdbe.org/5cmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [https://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc 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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [https://pdbe.org/5cmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [https://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:15, 14 June 2023

OCA — Wed, 14 Jun 2023 12:15:45 GMT

←Older revision		Revision as of 12:15, 14 June 2023
Line 3:		Line 3:
	<StructureSection load='5cmc' size='340' side='right'caption='[[5cmc]], [[Resolution\|resolution]] 1.28Å' scene=''>		<StructureSection load='5cmc' size='340' side='right'caption='[[5cmc]], [[Resolution\|resolution]] 1.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cmc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~American_comb_jelly American comb jelly~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cmc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mnemiopsis_leidyi Mnemiopsis leidyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CMC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[4yki\|4yki]], [[5cmb\|5cmb]]</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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [https://pdbe.org/5cmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [https://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ML032222a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=27923 American comb jelly])</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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [~~http~~://pdbe.org/5cmc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0R4I973_MNELE A0A0R4I973_MNELE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: American comb jelly]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mayer, M L~~]]	+	[[Category: Mnemiopsis leidyi]]
-	[[Category: ~~Thomas, A~~]]	+	[[Category: Mayer ML]]
-	[[Category: ~~Glutamate receptor]]~~	+	[[Category: Thomas A]]
-	~~[[Category: Ion channel]]~~	+
-	~~[[Category: Membrane protein~~]]	+

OCA at 11:45, 27 March 2020

OCA — Fri, 27 Mar 2020 11:45:24 GMT

←Older revision		Revision as of 11:45, 27 March 2020
Line 1:		Line 1:

	==Mnemiopsis leidyi ML032222a iGluR LBD E423S mutant glycine complex==		==Mnemiopsis leidyi ML032222a iGluR LBD E423S mutant glycine complex==
-	<StructureSection load='5cmc' size='340' side='right' caption='[[5cmc]], [[Resolution\|resolution]] 1.28Å' scene=''>	+	<StructureSection load='5cmc' size='340' side='right'caption='[[5cmc]], [[Resolution\|resolution]] 1.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cmc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cmc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/American_comb_jelly American comb jelly]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CMC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[4yki\|4yki]], [[5cmb\|5cmb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yki\|4yki]], [[5cmb\|5cmb]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ML032222a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=27923 American comb jelly])</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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [http://pdbe.org/5cmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [http://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc 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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [http://pdbe.org/5cmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [http://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: American comb jelly]]
		+	[[Category: Large Structures]]
	[[Category: Mayer, M L]]		[[Category: Mayer, M L]]
	[[Category: Thomas, A]]		[[Category: Thomas, A]]

OCA at 20:03, 9 December 2016

OCA — Fri, 09 Dec 2016 20:03:57 GMT

←Older revision		Revision as of 20:03, 9 December 2016
Line 8:		Line 8:
	<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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [http://pdbe.org/5cmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [http://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc 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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [http://pdbe.org/5cmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [http://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The earliest metazoan ancestors of humans include the ctenophore Mnemiopsis leidyi The genome of this comb jelly encodes homologs of vertebrate ionotropic glutamate receptors (iGluRs) that are distantly related to glycine-activated NMDA receptors and that bind glycine with unusually high affinity. Using ligand-binding domain (LBD) mutants for electrophysiological analysis, we demonstrate that perturbing a ctenophore-specific interdomain Arg-Glu salt bridge that is notably absent from vertebrate AMPA, kainate, and NMDA iGluRs greatly increases the rate of recovery from desensitization, while biochemical analysis reveals a large decrease in affinity for glycine. X-ray crystallographic analysis details rearrangements in the binding pocket stemming from the mutations, and molecular dynamics simulations suggest that the interdomain salt bridge acts as a steric barrier regulating ligand binding and that the free energy required to access open conformations in the glycine-bound LBD is largely responsible for differences in ligand affinity among the LBD variants.
		+
		+	Molecular lock regulates binding of glycine to a primitive NMDA receptor.,Yu A, Alberstein R, Thomas A, Zimmet A, Grey R, Mayer ML, Lau AY Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):E6786-E6795. Epub 2016 Oct 17. PMID:27791085<ref>PMID:27791085</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5cmc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:28, 26 July 2016

OCA — Tue, 26 Jul 2016 15:28:26 GMT

←Older revision		Revision as of 15:28, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5cmc is ~~ON HOLD until Paper Publication~~	+	==Mnemiopsis leidyi ML032222a iGluR LBD E423S mutant glycine complex==
-		+	<StructureSection load='5cmc' size='340' side='right' caption='[[5cmc]], [[Resolution\|resolution]] 1.28Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5cmc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CMC FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yki\|4yki]], [[5cmb\|5cmb]]</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=5cmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cmc OCA], [http://pdbe.org/5cmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cmc RCSB], [http://www.ebi.ac.uk/pdbsum/5cmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cmc ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mayer, M L]]
		+	[[Category: Thomas, A]]
		+	[[Category: Glutamate receptor]]
		+	[[Category: Ion channel]]
		+	[[Category: Membrane protein]]

OCA at 11:33, 15 May 2016

OCA — Sun, 15 May 2016 11:33:07 GMT

←Older revision		Revision as of 11:33, 15 May 2016
Line 3:		Line 3:
	The entry 5cmc is ON HOLD until Paper Publication		The entry 5cmc is ON HOLD until Paper Publication

-	Authors: ~~Mayer, M.L., Thomas, A.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Mayer, M.L]]
-	[[Category: Thomas, A]]

OCA at 13:16, 12 August 2015

OCA — Wed, 12 Aug 2015 13:16:45 GMT

←Older revision		Revision as of 13:16, 12 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Mayer, M.L., Thomas, A.		Authors: Mayer, M.L., Thomas, A.

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

OCA — Wed, 22 Jul 2015 13:20:53 GMT

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

←Older revision

Revision as of 13:20, 22 July 2015

OCA: New page: '''Unreleased structure''' The entry 5cmc is ON HOLD Authors: Mayer, M.L., Thomas, A. Description: Category: Unreleased Structures Category: Mayer, M.L Category: Thomas, A

OCA — Wed, 22 Jul 2015 13:20:52 GMT

New page: '''Unreleased structure''' The entry 5cmc is ON HOLD Authors: Mayer, M.L., Thomas, A. Description: Category: Unreleased Structures Category: Mayer, M.L Category: Thomas, A

New page

'''Unreleased structure'''

The entry 5cmc is ON HOLD

Authors: Mayer, M.L., Thomas, A.

Description:
[[Category: Unreleased Structures]]
[[Category: Mayer, M.L]]
[[Category: Thomas, A]]