4x8a - Revision history

OCA at 11:29, 9 May 2024

OCA — Thu, 09 May 2024 11:29:25 GMT

←Older revision		Revision as of 11:29, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x8a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetococcus_marinus_MC-1 Magnetococcus marinus MC-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x8a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetococcus_marinus_MC-1 Magnetococcus marinus MC-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X8A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2CV:HEGA-10'>2CV</scene>, <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 3.02Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2CV:HEGA-10'>2CV</scene>, <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4x8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x8a OCA], [https://pdbe.org/4x8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x8a RCSB], [https://www.ebi.ac.uk/pdbsum/4x8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x8a 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=4x8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x8a OCA], [https://pdbe.org/4x8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x8a RCSB], [https://www.ebi.ac.uk/pdbsum/4x8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x8a ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:17, 12 April 2023

OCA — Wed, 12 Apr 2023 21:17:16 GMT

←Older revision		Revision as of 21:17, 12 April 2023
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	<StructureSection load='4x8a' size='340' side='right'caption='[[4x8a]], [[Resolution\|resolution]] 3.02Å' scene=''>		<StructureSection load='4x8a' size='340' side='right'caption='[[4x8a]], [[Resolution\|resolution]] 3.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x8a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X8A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X8A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x8a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetococcus_marinus_MC-1 Magnetococcus marinus MC-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X8A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2CV:HEGA-10'>2CV</scene>, <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2CV:HEGA-10'>2CV</scene>, <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x87\|4x87]], [[3zjz\|3zjz]], [[4cbc\|4cbc]], [[4x89\|4x89]], [[4x88\|4x88]]~~</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=4x8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x8a OCA], [https://pdbe.org/4x8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x8a RCSB], [https://www.ebi.ac.uk/pdbsum/4x8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x8a 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=4x8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x8a OCA], [~~http~~://pdbe.org/4x8a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x8a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x8a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x8a ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0L5S6_MAGMM A0L5S6_MAGMM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4x8a" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x8a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bagneris, C~~]]	+	[[Category: Magnetococcus marinus MC-1]]
-	[[Category: ~~Naylor,~~ C E]]	+	[[Category: Bagneris C]]
-	[[Category: ~~Wallace, B A~~]]	+	[[Category: Naylor CE]]
-	[[Category: ~~Membrane protein]]~~	+	[[Category: Wallace BA]]
-	~~[[Category: Selectivity filter]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 00:02, 6 June 2019

OCA — Thu, 06 Jun 2019 00:02:26 GMT

←Older revision		Revision as of 00:02, 6 June 2019
Line 1:		Line 1:

	==NavMS pore and C-terminal domain grown from protein purified in LiCl==		==NavMS pore and C-terminal domain grown from protein purified in LiCl==
-	<StructureSection load='4x8a' size='340' side='right' caption='[[4x8a]], [[Resolution\|resolution]] 3.02Å' scene=''>	+	<StructureSection load='4x8a' size='340' side='right'caption='[[4x8a]], [[Resolution\|resolution]] 3.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x8a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x8a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X8A FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bagneris, C]]		[[Category: Bagneris, C]]
	[[Category: Naylor, C E]]		[[Category: Naylor, C E]]

OCA at 02:32, 13 July 2016

OCA — Wed, 13 Jul 2016 02:32:41 GMT

←Older revision		Revision as of 02:32, 13 July 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2CV:HEGA-10'>2CV</scene>, <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2CV:HEGA-10'>2CV</scene>, <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x87\|4x87]], [[3zjz\|3zjz]], [[4cbc\|4cbc]], [[4x89\|4x89]], [[4x88\|4x88]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x87\|4x87]], [[3zjz\|3zjz]], [[4cbc\|4cbc]], [[4x89\|4x89]], [[4x88\|4x88]]</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=4x8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x8a OCA], [http://pdbe.org/4x8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x8a RCSB], [http://www.ebi.ac.uk/pdbsum/4x8a PDBsum]</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=4x8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x8a OCA], [http://pdbe.org/4x8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x8a RCSB], [http://www.ebi.ac.uk/pdbsum/4x8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x8a ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:45, 23 June 2016

OCA — Thu, 23 Jun 2016 15:45:33 GMT

←Older revision		Revision as of 15:45, 23 June 2016
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Voltage-gated sodium channels ~~have~~ essential ~~roles in~~ electrical signalling. ~~Prokaryotic~~ sodium ~~channels are tetramers consisting of transmembrane (TM) voltage-sensing and pore domains~~, ~~and a cytoplasmic carboxy-terminal domain. Previous crystal structures of bacterial sodium channels revealed~~ the ~~nature~~ of ~~their TM domains but not their C-terminal domains (CTDs)~~. ~~Here, using electron paramagnetic resonance (EPR) spectroscopy combined with molecular dynamics, we show that~~ the ~~CTD of~~ the ~~NavMs channel from Magnetococcus marinus includes a flexible region linking the TM domains to a four-helix coiled-coil bundle. A 2.9 A resolution~~ crystal structure of the ~~NavMs pore indicates~~ the ~~position~~ of the ~~CTD, which is consistent with the EPR-derived structure. Functional analyses demonstrate that the coiled-coil domain couples inactivation with~~ channel ~~opening, and is enabled by negatively charged residues in the linker region~~. ~~A mechanism for gating is proposed~~ based on the structure, ~~whereby splaying of~~ the ~~bottom of~~ the ~~pore~~ is ~~possible without requiring unravelling~~ of the ~~coiled-coil~~.	+	Voltage-gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na+ approximately Li+ >> K+, Ca2+, Mg2+) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.

-	~~Role~~ of ~~the C~~-~~terminal domain in the structure and function of tetrameric~~ sodium ~~channels~~.,Bagneris C, ~~Decaen~~ PG, ~~Hall BA~~, ~~Naylor CE~~, Clapham DE~~, Kay CW~~, Wallace BA ~~Nat Commun~~. ~~2013 Sep 20;4:2465~~. ~~doi~~: ~~10.1038/ncomms3465~~. PMID:~~24051986~~<ref>PMID:~~24051986~~</ref>	+	Molecular basis of ion permeability in a voltage-gated sodium channel.,Naylor CE, Bagneris C, DeCaen PG, Sula A, Scaglione A, Clapham DE, Wallace BA EMBO J. 2016 Feb 12. pii: e201593285. PMID:26873592<ref>PMID:26873592</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 03:37, 10 March 2016

OCA — Thu, 10 Mar 2016 03:37:24 GMT

←Older revision		Revision as of 03:37, 10 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4x8a is ~~ON HOLD until Paper~~ Publication	+	==NavMS pore and C-terminal domain grown from protein purified in LiCl==
		+	<StructureSection load='4x8a' size='340' side='right' caption='[[4x8a]], [[Resolution\|resolution]] 3.02Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x8a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X8A FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2CV:HEGA-10'>2CV</scene>, <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x87\|4x87]], [[3zjz\|3zjz]], [[4cbc\|4cbc]], [[4x89\|4x89]], [[4x88\|4x88]]</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=4x8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x8a OCA], [http://pdbe.org/4x8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x8a RCSB], [http://www.ebi.ac.uk/pdbsum/4x8a PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Voltage-gated sodium channels have essential roles in electrical signalling. Prokaryotic sodium channels are tetramers consisting of transmembrane (TM) voltage-sensing and pore domains, and a cytoplasmic carboxy-terminal domain. Previous crystal structures of bacterial sodium channels revealed the nature of their TM domains but not their C-terminal domains (CTDs). Here, using electron paramagnetic resonance (EPR) spectroscopy combined with molecular dynamics, we show that the CTD of the NavMs channel from Magnetococcus marinus includes a flexible region linking the TM domains to a four-helix coiled-coil bundle. A 2.9 A resolution crystal structure of the NavMs pore indicates the position of the CTD, which is consistent with the EPR-derived structure. Functional analyses demonstrate that the coiled-coil domain couples inactivation with channel opening, and is enabled by negatively charged residues in the linker region. A mechanism for gating is proposed based on the structure, whereby splaying of the bottom of the pore is possible without requiring unravelling of the coiled-coil.

-	~~Authors: Naylor,~~ C.E., Bagneris, C., ~~Wallace~~, B.A.	+	Role of the C-terminal domain in the structure and function of tetrameric sodium channels.,Bagneris C, Decaen PG, Hall BA, Naylor CE, Clapham DE, Kay CW, Wallace BA Nat Commun. 2013 Sep 20;4:2465. doi: 10.1038/ncomms3465. PMID:24051986<ref>PMID:24051986</ref>

-	~~Description: NavMS pore and C-terminal domain grown from protein purified in LiCl~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Wallace, B.A]]~~	+	<div class="pdbe-citations 4x8a" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bagneris, C]]		[[Category: Bagneris, C]]
-	[[Category: Naylor, C.E]]	+	[[Category: Naylor, C E]]
		+	[[Category: Wallace, B A]]
		+	[[Category: Membrane protein]]
		+	[[Category: Selectivity filter]]
		+	[[Category: Transport protein]]

OCA at 20:38, 24 December 2014

OCA — Wed, 24 Dec 2014 20:38:20 GMT

←Older revision		Revision as of 20:38, 24 December 2014
Line 6:		Line 6:

	Description: NavMS pore and C-terminal domain grown from protein purified in LiCl		Description: NavMS pore and C-terminal domain grown from protein purified in LiCl
		+	[[Category: Unreleased Structures]]
		+	[[Category: Wallace, B.A]]
		+	[[Category: Bagneris, C]]
		+	[[Category: Naylor, C.E]]

OCA: Protected "4x8a" [edit=sysop:move=sysop]

OCA — Wed, 17 Dec 2014 11:46:52 GMT

Protected "4x8a" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:46, 17 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x8a is ON HOLD until Paper Publication Authors: Naylor, C.E., Bagneris, C., Wallace, B.A. Description: NavMS pore and C-terminal domain grown from...

OCA — Wed, 17 Dec 2014 11:46:50 GMT

New page: '''Unreleased structure''' The entry 4x8a is ON HOLD until Paper Publication Authors: Naylor, C.E., Bagneris, C., Wallace, B.A. Description: NavMS pore and C-terminal domain grown from...

New page

'''Unreleased structure'''

The entry 4x8a is ON HOLD until Paper Publication

Authors: Naylor, C.E., Bagneris, C., Wallace, B.A.

Description: NavMS pore and C-terminal domain grown from protein purified in LiCl