5ips - Revision history

OCA at 12:35, 6 March 2024

2024-03-06T12:35:13Z

← Older revision		Revision as of 12:35, 6 March 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/NMDZ1_XENLA NMDZ1_XENLA] Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:16214956, PubMed:19524674, PubMed:21677647, PubMed:25008524, PubMed:26912815, PubMed:27135925, Ref.11, PubMed:28232581). Sensitivity to glutamate and channel kinetics depend on the subunit composition (Probable).<ref>PMID:16214956</ref> <ref>PMID:19524674</ref> <ref>PMID:21677647</ref> <ref>PMID:25008524</ref> <ref>PMID:26912815</ref> <ref>PMID:27135925</ref> <ref>PMID:28232581</ref> [PDB:5IOV]		[https://www.uniprot.org/uniprot/NMDZ1_XENLA NMDZ1_XENLA] Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:16214956, PubMed:19524674, PubMed:21677647, PubMed:25008524, PubMed:26912815, PubMed:27135925, Ref.11, PubMed:28232581). Sensitivity to glutamate and channel kinetics depend on the subunit composition (Probable).<ref>PMID:16214956</ref> <ref>PMID:19524674</ref> <ref>PMID:21677647</ref> <ref>PMID:25008524</ref> <ref>PMID:26912815</ref> <ref>PMID:27135925</ref> <ref>PMID:28232581</ref> [PDB:5IOV]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated, calcium-permeable ion channels that mediate synaptic transmission and underpin learning and memory. NMDAR dysfunction is directly implicated in diseases ranging from seizure to ischemia. Despite its fundamental importance, little is known about how the NMDAR transitions between inactive and active states and how small molecules inhibit or activate ion channel gating. Here, we report electron cryo-microscopy structures of the GluN1-GluN2B NMDA receptor in an ensemble of competitive antagonist-bound states, an agonist-bound form, and a state bound with agonists and the allosteric inhibitor Ro25-6981. Together with double electron-electron resonance experiments, we show how competitive antagonists rupture the ligand binding domain (LBD) gating "ring," how agonists retain the ring in a dimer-of-dimers configuration, and how allosteric inhibitors, acting within the amino terminal domain, further stabilize the LBD layer. These studies illuminate how the LBD gating ring is fundamental to signal transduction and gating in NMDARs.

	Mechanism of NMDA Receptor Inhibition and Activation.,Zhu S, Stein RA, Yoshioka C, Lee CH, Goehring A, Mchaourab HS, Gouaux E Cell. 2016 Apr 21;165(3):704-14. doi: 10.1016/j.cell.2016.03.028. Epub 2016 Apr, 7. PMID:27062927<ref>PMID:27062927</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5ips" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==

OCA at 14:05, 30 August 2023

2023-08-30T14:05:30Z

← Older revision		Revision as of 14:05, 30 August 2023
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	<SX load='5ips' size='340' side='right' viewer='molstar' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>		<SX load='5ips' size='340' side='right' viewer='molstar' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~African_clawed_frog African clawed frog~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IPS FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5iou\|5iou]], [[5iov\|5iov]], [[5ipq\|5ipq]], [[5ipr\|5ipr]], [[5ipt\|5ipt]], [[5ipu\|5ipu]], [[5ipv\|5ipv]]</td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 13.5Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">NR2B ([http://www.ncbi.nlm~~.~~nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=8355 African clawed frog])~~</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=5ips FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ips OCA], [https://pdbe.org/5ips PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ips RCSB], [https://www.ebi.ac.uk/pdbsum/5ips PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ips 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=5ips FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ips OCA], [~~http~~://pdbe.org/5ips PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ips RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ips PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ips ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/NMDZ1_XENLA NMDZ1_XENLA] Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:16214956, PubMed:19524674, PubMed:21677647, PubMed:25008524, PubMed:26912815, PubMed:27135925, Ref.11, PubMed:28232581). Sensitivity to glutamate and channel kinetics depend on the subunit composition (Probable).<ref>PMID:16214956</ref> <ref>PMID:19524674</ref> <ref>PMID:21677647</ref> <ref>PMID:25008524</ref> <ref>PMID:26912815</ref> <ref>PMID:27135925</ref> <ref>PMID:28232581</ref> [PDB:5IOV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</SX>		</SX>
	~~[[Category: African clawed frog]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Goehring, A]]		[[Category: Xenopus laevis]]
	[[Category: Gouaux, E]]		[[Category: Goehring A]]
	[[Category: Lee~~, C H~~]]		[[Category: Gouaux E]]
	[[Category: Mchaourab~~, S H~~]]		[[Category: Lee CH]]
	[[Category: Stein~~, A R~~]]		[[Category: Mchaourab SH]]
	[[Category: Yoshioka, C]]		[[Category: Stein AR]]
	[[Category: Zhu, S]]		[[Category: Yoshioka C]]
	~~[[Category: Ligand-gated ion channel]]~~		[[Category: Zhu S]]
	~~[[Category: Signaling protein]]~~
	~~[[Category: Synaptic transmission~~]]

OCA at 20:15, 10 April 2020

2020-04-10T20:15:58Z

← Older revision		Revision as of 20:15, 10 April 2020
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	<SX load='5ips' size='340' side='right' viewer='molstar' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>		<SX load='5ips' size='340' side='right' viewer='molstar' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IPS FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iou\|5iou]], [[5iov\|5iov]], [[5ipq\|5ipq]], [[5ipr\|5ipr]], [[5ipt\|5ipt]], [[5ipu\|5ipu]], [[5ipv\|5ipv]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iou\|5iou]], [[5iov\|5iov]], [[5ipq\|5ipq]], [[5ipr\|5ipr]], [[5ipt\|5ipt]], [[5ipu\|5ipu]], [[5ipv\|5ipv]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR2B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR2B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</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=5ips FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ips OCA], [http://pdbe.org/5ips PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ips RCSB], [http://www.ebi.ac.uk/pdbsum/5ips PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ips 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=5ips FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ips OCA], [http://pdbe.org/5ips PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ips RCSB], [http://www.ebi.ac.uk/pdbsum/5ips PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ips ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:34, 6 March 2020

2020-03-06T18:34:33Z

← Older revision		Revision as of 18:34, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 4==		==Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 4==
	<~~StructureSection~~ load='5ips' size='340' side='right' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>		<SX load='5ips' size='340' side='right' viewer='molstar' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPS FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5ips" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ips" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Glutamate receptor 3D structures\|Glutamate receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</~~StructureSection~~>		</SX>
	[[Category: African clawed frog]]		[[Category: African clawed frog]]
			[[Category: Large Structures]]
	[[Category: Goehring, A]]		[[Category: Goehring, A]]
	[[Category: Gouaux, E]]		[[Category: Gouaux, E]]

OCA at 12:48, 16 November 2017

2017-11-16T12:48:02Z

← Older revision		Revision as of 12:48, 16 November 2017
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	<StructureSection load='5ips' size='340' side='right' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>		<StructureSection load='5ips' size='340' side='right' caption='[[5ips]], [[Resolution\|resolution]] 13.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ips]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPS FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iou\|5iou]], [[5iov\|5iov]], [[5ipq\|5ipq]], [[5ipr\|5ipr]], [[5ipt\|5ipt]], [[5ipu\|5ipu]], [[5ipv\|5ipv]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iou\|5iou]], [[5iov\|5iov]], [[5ipq\|5ipq]], [[5ipr\|5ipr]], [[5ipt\|5ipt]], [[5ipu\|5ipu]], [[5ipv\|5ipv]]</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=5ips FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ips OCA], [http://pdbe.org/5ips PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ips RCSB], [http://www.ebi.ac.uk/pdbsum/5ips PDBsum]</span></td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR2B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</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=5ips FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ips OCA], [http://pdbe.org/5ips PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ips RCSB], [http://www.ebi.ac.uk/pdbsum/5ips PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ips 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: African clawed frog]]
	[[Category: Goehring, A]]		[[Category: Goehring, A]]
	[[Category: Gouaux, E]]		[[Category: Gouaux, E]]

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

2016-05-10T19:19:16Z

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

← Older revision	Revision as of 19:19, 10 May 2016
(No difference)

OCA: New page: ==Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 4==