5yua - Revision history

OCA at 08:37, 22 November 2023

OCA — Wed, 22 Nov 2023 08:37:53 GMT

←Older revision		Revision as of 08:37, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of voltage-gated sodium channel NavAb in high-pH condition==		==Crystal structure of voltage-gated sodium channel NavAb in high-pH condition==
-	<StructureSection load='5yua' size='340' side='right' caption='[[5yua]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5yua' size='340' side='right'caption='[[5yua]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yua]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_49616 Atcc 49616~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yua]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliarcobacter_butzleri Aliarcobacter butzleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YUA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PX4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PX4</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]] 2.8008556Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAMEA4475700_01771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28197 ATCC 49616])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PX4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PX4</scene></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=5yua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yua OCA], [~~http~~://pdbe.org/5yua PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yua RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yua PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yua 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=5yua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yua OCA], [https://pdbe.org/5yua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yua RCSB], [https://www.ebi.ac.uk/pdbsum/5yua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yua ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A8EVM5_ALIB4 A8EVM5_ALIB4]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5yua" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yua" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 49616~~]]	+	[[Category: Aliarcobacter butzleri]]
-	[[Category: ~~Fujiyoshi, Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Irie, K~~]]	+	[[Category: Fujiyoshi Y]]
-	[[Category: ~~Shimomura, T~~]]	+	[[Category: Irie K]]
-	[[Category: ~~Ion channel]]~~	+	[[Category: Shimomura T]]
-	~~[[Category: Membrane protein~~]]	+

OCA at 08:21, 17 January 2018

OCA — Wed, 17 Jan 2018 08:21:02 GMT

←Older revision		Revision as of 08:21, 17 January 2018
Line 3:		Line 3:
	<StructureSection load='5yua' size='340' side='right' caption='[[5yua]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5yua' size='340' side='right' caption='[[5yua]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yua]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_49616 Atcc 49616]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YUA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PX4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PX4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PX4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PX4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAMEA4475700_01771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28197 ATCC 49616])</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=5yua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yua OCA], [http://pdbe.org/5yua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yua RCSB], [http://www.ebi.ac.uk/pdbsum/5yua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yua 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=5yua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yua OCA], [http://pdbe.org/5yua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yua RCSB], [http://www.ebi.ac.uk/pdbsum/5yua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yua ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Voltage-gated sodium channels are crucial for electro-signalling in living systems. Analysis of the molecular mechanism requires both fine electrophysiological evaluation and high-resolution channel structures. Here, we optimized a dual expression system of NavAb, which is a well-established standard of prokaryotic voltage-gated sodium channels, for E. coli and insect cells using a single plasmid vector to analyse high-resolution protein structures and measure large ionic currents. Using this expression system, we evaluated the voltage dependence and determined the crystal structures of NavAb wild-type and two mutants, E32Q and N49K, whose voltage dependence were positively shifted and essential interactions were lost in voltage sensor domain. The structural and functional comparison elucidated the molecular mechanisms of the voltage dependence of prokaryotic voltage-gated sodium channels.
		+
		+	Optimized expression and purification of NavAb provide the structural insight into the voltage dependence.,Irie K, Haga Y, Shimomura T, Fujiyoshi Y FEBS Lett. 2017 Dec 22. doi: 10.1002/1873-3468.12955. PMID:29274127<ref>PMID:29274127</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yua" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 49616]]
	[[Category: Fujiyoshi, Y]]		[[Category: Fujiyoshi, Y]]
	[[Category: Irie, K]]		[[Category: Irie, K]]

OCA at 08:35, 27 December 2017

OCA — Wed, 27 Dec 2017 08:35:42 GMT

←Older revision		Revision as of 08:35, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yua is ~~ON HOLD~~	+	==Crystal structure of voltage-gated sodium channel NavAb in high-pH condition==
-		+	<StructureSection load='5yua' size='340' side='right' caption='[[5yua]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~: ~~Irie~~, K., ~~Shimomura~~, T., ~~Fujiyosih~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yua]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YUA FirstGlance]. <br>
-	~~Description: Prokaryotic voltage gated sodium channel~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PX4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PX4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5yua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yua OCA], [http://pdbe.org/5yua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yua RCSB], [http://www.ebi.ac.uk/pdbsum/5yua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yua ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fujiyoshi, Y]]
	[[Category: Irie, K]]		[[Category: Irie, K]]
-	[[Category: Fujiyosih, Y]]
	[[Category: Shimomura, T]]		[[Category: Shimomura, T]]
		+	[[Category: Ion channel]]
		+	[[Category: Membrane protein]]

OCA at 05:56, 6 December 2017

OCA — Wed, 06 Dec 2017 05:56:54 GMT

←Older revision		Revision as of 05:56, 6 December 2017
Line 5:		Line 5:
	Authors: Irie, K., Shimomura, T., Fujiyosih, Y.		Authors: Irie, K., Shimomura, T., Fujiyosih, Y.

-	Description: ~~prokaryotic~~ voltage gated sodium channel	+	Description: Prokaryotic voltage gated sodium channel
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Irie, K]]		[[Category: Irie, K]]
	[[Category: Fujiyosih, Y]]		[[Category: Fujiyosih, Y]]
	[[Category: Shimomura, T]]		[[Category: Shimomura, T]]

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

OCA — Wed, 29 Nov 2017 04:59:15 GMT

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

←Older revision

Revision as of 04:59, 29 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yua is ON HOLD Authors: Irie, K., Shimomura, T., Fujiyosih, Y. Description: prokaryotic voltage gated sodium channel [[Category: Unreleased Struct...

OCA — Wed, 29 Nov 2017 04:59:14 GMT

New page: '''Unreleased structure''' The entry 5yua is ON HOLD Authors: Irie, K., Shimomura, T., Fujiyosih, Y. Description: prokaryotic voltage gated sodium channel [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 5yua is ON HOLD

Authors: Irie, K., Shimomura, T., Fujiyosih, Y.

Description: prokaryotic voltage gated sodium channel
[[Category: Unreleased Structures]]
[[Category: Irie, K]]
[[Category: Fujiyosih, Y]]
[[Category: Shimomura, T]]