6ud3 - Revision history

OCA at 09:29, 20 March 2024

OCA — Wed, 20 Mar 2024 09:29:20 GMT

←Older revision		Revision as of 09:29, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='6ud3' size='340' side='right'caption='[[6ud3]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='6ud3' size='340' side='right'caption='[[6ud3]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ud3]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UD3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6UD3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ud3]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UD3 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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RI5:(1AR,2AR,3S,6R,6AS,8AS,8BR,9R)-2A-HYDROXY-8B-METHYL-9-(PROP-1-EN-2-YL)HEXAHYDRO-3,6-METHANO-1,5,7-TRIOXACYCLOPENTA[IJ]CYCLOPROPA[A]AZULENE-4,8(3H)-DIONE'>RI5</scene>~~</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]] 3.5Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glra1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])~~</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RI5:(1AR,2AR,3S,6R,6AS,8AS,8BR,9R)-2A-HYDROXY-8B-METHYL-9-(PROP-1-EN-2-YL)HEXAHYDRO-3,6-METHANO-1,5,7-TRIOXACYCLOPENTA[IJ]CYCLOPROPA[A]AZULENE-4,8(3H)-DIONE'>RI5</scene></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=6ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ud3 OCA], [~~http~~://pdbe.org/6ud3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ud3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ud3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ud3 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=6ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ud3 OCA], [https://pdbe.org/6ud3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ud3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ud3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ud3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLRA1_DANRE GLRA1_DANRE]] Glycine receptors are ligand-gated chloride channels. Channel opening is triggered by extracellular glycine (PubMed:10188956, PubMed:26344198). Plays an important role in the down-regulation of neuronal excitability. Contributes to the generation of inhibitory postsynaptic currents. Channel activity is potentiated by ethanol (By similarity).[UniProtKB:P23415]<ref>PMID:10188956</ref> <ref>PMID:26344198</ref>	+	[https://www.uniprot.org/uniprot/GLRA1_DANRE GLRA1_DANRE] Glycine receptors are ligand-gated chloride channels. Channel opening is triggered by extracellular glycine (PubMed:10188956, PubMed:26344198). Plays an important role in the down-regulation of neuronal excitability. Contributes to the generation of inhibitory postsynaptic currents. Channel activity is potentiated by ethanol (By similarity).[UniProtKB:P23415]<ref>PMID:10188956</ref> <ref>PMID:26344198</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.	+
-		+
-	Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs.,Kumar A, Basak S, Rao S, Gicheru Y, Mayer ML, Sansom MSP, Chakrapani S Nat Commun. 2020 Jul 27;11(1):3752. doi: 10.1038/s41467-020-17364-5. PMID:32719334<ref>PMID:32719334</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6ud3" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basak, S]]	+	[[Category: Basak S]]
-	[[Category: Chakrapani, S]]	+	[[Category: Chakrapani S]]
-	[[Category: Kumar, A]]	+	[[Category: Kumar A]]
-	~~[[Category: Glycine receptor recombinant proteins glycine]]~~	+
-	~~[[Category: Ions ligands receptor]]~~	+
-	~~[[Category: Membrane protein~~]]	+

OCA at 10:02, 12 August 2020

OCA — Wed, 12 Aug 2020 10:02:36 GMT

←Older revision		Revision as of 10:02, 12 August 2020
Line 1:		Line 1:

	==Full length Glycine receptor reconstituted in lipid nanodisc in Gly/PTX-bound open/blocked conformation==		==Full length Glycine receptor reconstituted in lipid nanodisc in Gly/PTX-bound open/blocked conformation==
-	<StructureSection load='6ud3' size='340' side='right'caption='[[6ud3]]' scene=''>	+	<StructureSection load='6ud3' size='340' side='right'caption='[[6ud3]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UD3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UD3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ud3]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UD3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UD3 FirstGlance]. <br>
-	</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=6ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ud3 OCA], [http://pdbe.org/6ud3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ud3 RCSB], [http://www.ebi.ac.uk/pdbsum/6ud3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ud3 ProSAT]</span></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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RI5:(1AR,2AR,3S,6R,6AS,8AS,8BR,9R)-2A-HYDROXY-8B-METHYL-9-(PROP-1-EN-2-YL)HEXAHYDRO-3,6-METHANO-1,5,7-TRIOXACYCLOPENTA[IJ]CYCLOPROPA[A]AZULENE-4,8(3H)-DIONE'>RI5</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glra1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=6ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ud3 OCA], [http://pdbe.org/6ud3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ud3 RCSB], [http://www.ebi.ac.uk/pdbsum/6ud3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ud3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLRA1_DANRE GLRA1_DANRE]] Glycine receptors are ligand-gated chloride channels. Channel opening is triggered by extracellular glycine (PubMed:10188956, PubMed:26344198). Plays an important role in the down-regulation of neuronal excitability. Contributes to the generation of inhibitory postsynaptic currents. Channel activity is potentiated by ethanol (By similarity).[UniProtKB:P23415]<ref>PMID:10188956</ref> <ref>PMID:26344198</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.
		+
		+	Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs.,Kumar A, Basak S, Rao S, Gicheru Y, Mayer ML, Sansom MSP, Chakrapani S Nat Commun. 2020 Jul 27;11(1):3752. doi: 10.1038/s41467-020-17364-5. PMID:32719334<ref>PMID:32719334</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ud3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basak S]]	+	[[Category: Basak, S]]
-	[[Category: Chakrapani S]]	+	[[Category: Chakrapani, S]]
-	[[Category: Kumar A]]	+	[[Category: Kumar, A]]
		+	[[Category: Glycine receptor recombinant proteins glycine]]
		+	[[Category: Ions ligands receptor]]
		+	[[Category: Membrane protein]]

OCA at 11:09, 29 July 2020

OCA — Wed, 29 Jul 2020 11:09:15 GMT

←Older revision		Revision as of 11:09, 29 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ud3 is ~~ON HOLD~~	+	==Full length Glycine receptor reconstituted in lipid nanodisc in Gly/PTX-bound open/blocked conformation==
-		+	<StructureSection load='6ud3' size='340' side='right'caption='[[6ud3]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UD3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UD3 FirstGlance]. <br>
-	~~Description~~:	+	</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=6ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ud3 OCA], [http://pdbe.org/6ud3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ud3 RCSB], [http://www.ebi.ac.uk/pdbsum/6ud3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ud3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Basak S]]
		+	[[Category: Chakrapani S]]
		+	[[Category: Kumar A]]

OCA at 04:22, 6 May 2020

OCA — Wed, 06 May 2020 04:22:31 GMT

←Older revision		Revision as of 04:22, 6 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ud3 is ON HOLD ~~until Paper Publication~~	+	The entry 6ud3 is ON HOLD

	Authors:		Authors:

OCA at 06:11, 5 February 2020

OCA — Wed, 05 Feb 2020 06:11:30 GMT

←Older revision		Revision as of 06:11, 5 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ud3 is ON HOLD	+	The entry 6ud3 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 03:55, 10 October 2019

OCA — Thu, 10 Oct 2019 03:55:59 GMT

←Older revision		Revision as of 03:55, 10 October 2019
Line 3:		Line 3:
	The entry 6ud3 is ON HOLD		The entry 6ud3 is ON HOLD

-	Authors: ~~Kumar, A., Chakrapani, S.~~	+	Authors:

-	Description: ~~Membrane protein P conformation~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chakrapani, S]]
-	[[Category: Kumar, A]]

OCA: Protected "6ud3" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 08:37:30 GMT

Protected "6ud3" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:37, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6ud3 is ON HOLD Authors: Kumar, A., Chakrapani, S. Description: Membrane protein P conformation Category: Unreleased Structures [[Category: Cha...

OCA — Wed, 02 Oct 2019 08:37:29 GMT

New page: '''Unreleased structure''' The entry 6ud3 is ON HOLD Authors: Kumar, A., Chakrapani, S. Description: Membrane protein P conformation Category: Unreleased Structures [[Category: Cha...

New page

'''Unreleased structure'''

The entry 6ud3 is ON HOLD

Authors: Kumar, A., Chakrapani, S.

Description: Membrane protein P conformation
[[Category: Unreleased Structures]]
[[Category: Chakrapani, S]]
[[Category: Kumar, A]]