7l6u - Revision history

OCA at 14:58, 6 March 2024

OCA — Wed, 06 Mar 2024 14:58:58 GMT

←Older revision		Revision as of 14:58, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='7l6u' size='340' side='right'caption='[[7l6u]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='7l6u' size='340' side='right'caption='[[7l6u]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7l6u]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Dicd3 Dicd3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L6U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7l6u]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_dadantii_3937 Dickeya dadantii 3937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L6U FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Dda3937_00520 (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=198628 DICD3])~~</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]] 3.3Å</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=7l6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l6u OCA], [https://pdbe.org/7l6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l6u RCSB], [https://www.ebi.ac.uk/pdbsum/7l6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l6u 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=7l6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l6u OCA], [https://pdbe.org/7l6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l6u RCSB], [https://www.ebi.ac.uk/pdbsum/7l6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l6u ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/E0SJQ4_DICD3 E0SJQ4_DICD3]
-	Although it has long been proposed that membrane proteins may contain tightly bound lipids, their identity, the structure of their binding sites, and their functional and structural relevance have remained elusive. To some extent, this is because tightly bound lipids are often located at the periphery of proteins, where the quality of density maps is usually poorer, and because they may be outcompeted by detergent molecules used during standard purification procedures. As a step toward characterizing natively bound lipids in the superfamily of pentameric ligand-gated ion channels (pLGICs), we applied single-particle cryogenic electron microscopy to fragments of native membrane obtained in the complete absence of detergent-solubilization steps. Because of the heterogeneous lipid composition of membranes in the secretory pathway of eukaryotic cells, we chose to study a bacterial pLGIC (ELIC) expressed in Escherichia coli's inner membrane. We obtained a three-dimensional reconstruction of unliganded ELIC (2.5-A resolution) that shows clear evidence for two types of tightly bound lipid at the protein-bulk-membrane interface. One of them was consistent with a "regular" diacylated phospholipid, in the cytoplasmic leaflet, whereas the other one was consistent with the tetra-acylated structure of cardiolipin, in the periplasmic leaflet. Upon reconstitution in E. coli polar-lipid bilayers, ELIC retained the functional properties characteristic of members of this superfamily, and thus, the fitted atomic model is expected to represent the (long-debated) unliganded-closed, "resting" conformation of this ion channel. Notably, the addition of cardiolipin to phosphatidylcholine membranes restored the ion-channel activity that is largely lost in phosphatidylcholine-only bilayers.	+
-		+
-	~~Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel.,Kumar P, Cymes GD, Grosman C Proc Natl Acad Sci U S A. 2021 Jun 8;118(23). pii~~: ~~2100164118. doi:, 10.1073~~/~~pnas.2100164118. PMID:34083441<ref>PMID:34083441<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7l6u" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dicd3~~]]	+	[[Category: Dickeya dadantii 3937]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grosman, C]]	+	[[Category: Grosman C]]
-	[[Category: Kumar, P]]	+	[[Category: Kumar P]]
-	~~[[Category: Cys-loop receptor]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Nanodisc]]~~	+
-	~~[[Category: Pentameric ligand-gated ion channel]]~~	+
-	~~[[Category: Protein-lipid interface]]~~	+
-	~~[[Category: Styrene maleic acid copolymer~~]]	+

OCA at 10:10, 14 July 2021

OCA — Wed, 14 Jul 2021 10:10:10 GMT

←Older revision		Revision as of 10:10, 14 July 2021
Line 1:		Line 1:

	==Unliganded ELIC in POPC-only nanodiscs at 3.3-Angstrom resolution==		==Unliganded ELIC in POPC-only nanodiscs at 3.3-Angstrom resolution==
-	<StructureSection load='7l6u' size='340' side='right'caption='[[7l6u]]' scene=''>	+	<StructureSection load='7l6u' size='340' side='right'caption='[[7l6u]], [[Resolution\|resolution]] 3.30Å' 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=7L6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L6U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7l6u]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Dicd3 Dicd3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L6U FirstGlance]. <br>
-	</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=7l6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l6u OCA], [https://pdbe.org/7l6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l6u RCSB], [https://www.ebi.ac.uk/pdbsum/7l6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l6u ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dda3937_00520 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198628 DICD3])</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=7l6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l6u OCA], [https://pdbe.org/7l6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l6u RCSB], [https://www.ebi.ac.uk/pdbsum/7l6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l6u ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although it has long been proposed that membrane proteins may contain tightly bound lipids, their identity, the structure of their binding sites, and their functional and structural relevance have remained elusive. To some extent, this is because tightly bound lipids are often located at the periphery of proteins, where the quality of density maps is usually poorer, and because they may be outcompeted by detergent molecules used during standard purification procedures. As a step toward characterizing natively bound lipids in the superfamily of pentameric ligand-gated ion channels (pLGICs), we applied single-particle cryogenic electron microscopy to fragments of native membrane obtained in the complete absence of detergent-solubilization steps. Because of the heterogeneous lipid composition of membranes in the secretory pathway of eukaryotic cells, we chose to study a bacterial pLGIC (ELIC) expressed in Escherichia coli's inner membrane. We obtained a three-dimensional reconstruction of unliganded ELIC (2.5-A resolution) that shows clear evidence for two types of tightly bound lipid at the protein-bulk-membrane interface. One of them was consistent with a "regular" diacylated phospholipid, in the cytoplasmic leaflet, whereas the other one was consistent with the tetra-acylated structure of cardiolipin, in the periplasmic leaflet. Upon reconstitution in E. coli polar-lipid bilayers, ELIC retained the functional properties characteristic of members of this superfamily, and thus, the fitted atomic model is expected to represent the (long-debated) unliganded-closed, "resting" conformation of this ion channel. Notably, the addition of cardiolipin to phosphatidylcholine membranes restored the ion-channel activity that is largely lost in phosphatidylcholine-only bilayers.
		+
		+	Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel.,Kumar P, Cymes GD, Grosman C Proc Natl Acad Sci U S A. 2021 Jun 8;118(23). pii: 2100164118. doi:, 10.1073/pnas.2100164118. PMID:34083441<ref>PMID:34083441</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7l6u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dicd3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grosman C]]	+	[[Category: Grosman, C]]
-	[[Category: Kumar P]]	+	[[Category: Kumar, P]]
		+	[[Category: Cys-loop receptor]]
		+	[[Category: Membrane protein]]
		+	[[Category: Nanodisc]]
		+	[[Category: Pentameric ligand-gated ion channel]]
		+	[[Category: Protein-lipid interface]]
		+	[[Category: Styrene maleic acid copolymer]]

OCA at 07:32, 25 June 2021

OCA — Fri, 25 Jun 2021 07:32:31 GMT

←Older revision		Revision as of 07:32, 25 June 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7l6u ~~is ON HOLD until Paper Publication~~	+	==Unliganded ELIC in POPC-only nanodiscs at 3.3-Angstrom resolution==
-		+	<StructureSection load='7l6u' size='340' side='right'caption='[[7l6u]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L6U FirstGlance]. <br>
-	~~Description~~:	+	</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=7l6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l6u OCA], [https://pdbe.org/7l6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l6u RCSB], [https://www.ebi.ac.uk/pdbsum/7l6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l6u ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Grosman C]]
		+	[[Category: Kumar P]]

OCA at 09:13, 10 February 2021

OCA — Wed, 10 Feb 2021 09:13:25 GMT

←Older revision		Revision as of 09:13, 10 February 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7l6u is ON HOLD	+	The entry 7l6u is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7l6u" [edit=sysop:move=sysop]

OCA — Wed, 30 Dec 2020 05:34:05 GMT

Protected "7l6u" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:34, 30 December 2020

OCA: New page: '''Unreleased structure''' The entry 7l6u is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Dec 2020 05:34:04 GMT

New page: '''Unreleased structure''' The entry 7l6u is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7l6u is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]