6vxo - Revision history

OCA at 14:40, 6 March 2024

OCA — Wed, 06 Mar 2024 14:40:32 GMT

←Older revision		Revision as of 14:40, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6vxo' size='340' side='right'caption='[[6vxo]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='6vxo' size='340' side='right'caption='[[6vxo]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vxo]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VXO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VXO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vxo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VXO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=POV:(2S)-3-(HEXADECANOYLOXY)-2-~~[~~(9Z)-OCTADEC-9-ENOYLOXY~~]~~PROPYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>POV</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">~~BH1501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN~~])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=POV:(2S)-3-(HEXADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>POV</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=6vxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vxo OCA], [~~http~~://pdbe.org/6vxo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vxo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vxo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vxo 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=6vxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vxo OCA], [https://pdbe.org/6vxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vxo RCSB], [https://www.ebi.ac.uk/pdbsum/6vxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vxo ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Disease ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/SCN9A_HUMAN SCN9A_HUMAN] Channelopathy-associated congenital insensitivity to pain;Dravet syndrome;Primary erythromelalgia;Sodium channelopathy-related small fiber neuropathy;Generalized epilepsy with febrile seizures-plus;Hereditary sensory and autonomic neuropathy type 2;Paroxysmal extreme pain disorder;Erythromelalgia. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
-	~~NaChBac, the first bacterial voltage~~-~~gated Na(+) (Nav) channel~~ to ~~be characterized, has been the prokaryotic prototype for studying the structure~~-~~function relationship of Nav channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the single particle electron cryomicroscopy (cryo~~-~~EM) analysis of NaChBac in both detergent micelles~~ and ~~nanodiscs~~. ~~Under both conditions, the conformation of NaChBac~~ is ~~nearly identical to that of~~ the ~~potentially inactivated NavAb~~. ~~Determining~~ the ~~structure of NaChBac~~ in ~~nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav channels in lipid bilayers~~. ~~To study GMTs in mammalian Nav channels, we generated a chimera in which~~ the ~~extracellular fragment of the S3 and S4 segments~~ in ~~the second voltage-sensing domain from Nav1~~.~~7 replaced~~ the ~~corresponding sequence~~ in ~~NaChBac~~. ~~Cryo-EM structures of~~ the ~~nanodisc-embedded chimera alone and~~ in ~~complex with HuwenToxin IV (HWTX-IV) were determined to 3~~.~~5 and 3~~.~~2 A resolutions, respectively~~. ~~Compared to~~ the ~~structure of HWTX~~-~~IV-bound human Nav1.7, which was obtained at an overall resolution~~ of 3.~~2 A,~~ the ~~local resolution of~~ the ~~toxin has been improved from approximately 6 to approximately 4 A. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of~~ the ~~interactions between GMTs and Nav channels in~~ a ~~membrane environment.~~	+	== Function ==
-		+	[https://www.uniprot.org/uniprot/SCN9A_HUMAN SCN9A_HUMAN] Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient (PubMed:7720699, PubMed:17167479, PubMed:25240195, PubMed:26680203, PubMed:15385606, PubMed:16988069, PubMed:17145499, PubMed:19369487, PubMed:24311784). It is a tetrodotoxin-sensitive Na(+) channel isoform (PubMed:7720699). Plays a role in pain mechanisms, especially in the development of inflammatory pain (PubMed:17167479, PubMed:17145499, PubMed:19369487, PubMed:24311784).<ref>PMID:15178348</ref> <ref>PMID:15385606</ref> <ref>PMID:16988069</ref> <ref>PMID:17145499</ref> <ref>PMID:17167479</ref> <ref>PMID:19369487</ref> <ref>PMID:24311784</ref> <ref>PMID:25240195</ref> <ref>PMID:26680203</ref> <ref>PMID:7720699</ref> [https://www.uniprot.org/uniprot/Q9KCR8_HALH5 Q9KCR8_HALH5]
-	~~Employing NaChBac for cryo~~-~~EM analysis of toxin action on voltage-gated~~ Na(+) ~~channels~~ in ~~nanodisc.~~,~~Gao S~~, ~~Valinsky WC~~, ~~On NC~~, ~~Houlihan PR~~, ~~Qu Q~~, ~~Liu L~~, ~~Pan X~~, ~~Clapham DE, Yan N Proc Natl Acad Sci U S A~~. ~~2020 Jun 23;117~~(25):~~14187-14193~~. ~~doi~~:, 10.~~1073~~/~~pnas.1922903117. Epub 2020 Jun 8.~~ PMID:~~32513729~~<ref>PMID:~~32513729~~</ref>	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	</~~div~~>	+
-	<~~div class="pdbe-citations 6vxo" style="background-color~~:~~#fffaf0;"~~></~~div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Alkalihalobacillus halodurans C-125]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gao, S]]	+	[[Category: Gao S]]
-	[[Category: Yan, N]]	+	[[Category: Yan N]]
-	~~[[Category: Channel]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Nachbac]]~~	+
-	~~[[Category: Sodium ion-selective~~]]	+

OCA at 14:39, 8 July 2020

OCA — Wed, 08 Jul 2020 14:39:19 GMT

←Older revision		Revision as of 14:39, 8 July 2020
Line 1:		Line 1:

	==NaChBac-Nav1.7VSDII chimera in nanodisc==		==NaChBac-Nav1.7VSDII chimera in nanodisc==
-	<StructureSection load='6vxo' size='340' side='right'caption='[[6vxo]]' scene=''>	+	<StructureSection load='6vxo' size='340' side='right'caption='[[6vxo]], [[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=6VXO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VXO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vxo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VXO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VXO 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=6vxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vxo OCA], [http://pdbe.org/6vxo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vxo RCSB], [http://www.ebi.ac.uk/pdbsum/6vxo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vxo 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=POV:(2S)-3-(HEXADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>POV</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BH1501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6vxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vxo OCA], [http://pdbe.org/6vxo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vxo RCSB], [http://www.ebi.ac.uk/pdbsum/6vxo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vxo ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NaChBac, the first bacterial voltage-gated Na(+) (Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Nav channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the single particle electron cryomicroscopy (cryo-EM) analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav channels in lipid bilayers. To study GMTs in mammalian Nav channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaced the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 and 3.2 A resolutions, respectively. Compared to the structure of HWTX-IV-bound human Nav1.7, which was obtained at an overall resolution of 3.2 A, the local resolution of the toxin has been improved from approximately 6 to approximately 4 A. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Nav channels in a membrane environment.
		+
		+	Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na(+) channels in nanodisc.,Gao S, Valinsky WC, On NC, Houlihan PR, Qu Q, Liu L, Pan X, Clapham DE, Yan N Proc Natl Acad Sci U S A. 2020 Jun 23;117(25):14187-14193. doi:, 10.1073/pnas.1922903117. Epub 2020 Jun 8. PMID:32513729<ref>PMID:32513729</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vxo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gao S]]	+	[[Category: Gao, S]]
-	[[Category: Yan N]]	+	[[Category: Yan, N]]
		+	[[Category: Channel]]
		+	[[Category: Membrane protein]]
		+	[[Category: Nachbac]]
		+	[[Category: Sodium ion-selective]]

OCA at 06:26, 25 June 2020

OCA — Thu, 25 Jun 2020 06:26:16 GMT

←Older revision		Revision as of 06:26, 25 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vxo ~~is ON HOLD until Paper Publication~~	+	==NaChBac-Nav1.7VSDII chimera in nanodisc==
-		+	<StructureSection load='6vxo' size='340' side='right'caption='[[6vxo]]' scene=''>
-	~~Authors~~: ~~Yan~~, N., ~~Gao~~, S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VXO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VXO FirstGlance]. <br>
-	~~Description~~: ~~NaChBac~~-~~Nav1~~.~~7VSDII chimera in nanodisc~~	+	</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=6vxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vxo OCA], [http://pdbe.org/6vxo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vxo RCSB], [http://www.ebi.ac.uk/pdbsum/6vxo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vxo ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Gao, S]]	+	__TOC__
-	[[Category: Yan, N]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gao S]]
		+	[[Category: Yan N]]

OCA at 04:11, 22 April 2020

OCA — Wed, 22 Apr 2020 04:11:46 GMT

←Older revision		Revision as of 04:11, 22 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: ~~Nieng~~, Y., ~~Shuai~~, G.	+	Authors: Yan, N., Gao, S.

	Description: NaChBac-Nav1.7VSDII chimera in nanodisc		Description: NaChBac-Nav1.7VSDII chimera in nanodisc
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Shuai~~, G]]	+	[[Category: Gao, S]]
-	[[Category: ~~Nieng~~, Y]]	+	[[Category: Yan, N]]

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

OCA — Wed, 04 Mar 2020 05:38:14 GMT

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

←Older revision

Revision as of 05:38, 4 March 2020

OCA: New page: '''Unreleased structure''' The entry 6vxo is ON HOLD Authors: Nieng, Y., Shuai, G. Description: NaChBac-Nav1.7VSDII chimera in nanodisc Category: Unreleased Structures [[Category: ...

OCA — Wed, 04 Mar 2020 05:38:13 GMT

New page: '''Unreleased structure''' The entry 6vxo is ON HOLD Authors: Nieng, Y., Shuai, G. Description: NaChBac-Nav1.7VSDII chimera in nanodisc Category: Unreleased Structures [[Category: ...

New page

'''Unreleased structure'''

The entry 6vxo is ON HOLD

Authors: Nieng, Y., Shuai, G.

Description: NaChBac-Nav1.7VSDII chimera in nanodisc
[[Category: Unreleased Structures]]
[[Category: Shuai, G]]
[[Category: Nieng, Y]]