6u5p - Revision history

OCA at 09:28, 20 March 2024

OCA — Wed, 20 Mar 2024 09:28:40 GMT

←Older revision		Revision as of 09:28, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='6u5p' size='340' side='right'caption='[[6u5p]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6u5p' size='340' side='right'caption='[[6u5p]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u5p]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U5P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6U5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u5p]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U5P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 3.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>mthK, MTH_1520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~145262~~ "~~Methanobacterium thermoautotrophicus~~" ~~(sic) Zeikus and Wolfe 1972])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6u5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u5p OCA], [~~http~~://pdbe.org/6u5p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u5p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u5p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u5p 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=6u5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u5p OCA], [https://pdbe.org/6u5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u5p RCSB], [https://www.ebi.ac.uk/pdbsum/6u5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u5p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MTHK_METTH MTHK_METTH]] Calcium-gated potassium channel.	+	[https://www.uniprot.org/uniprot/MTHK_METTH MTHK_METTH] Calcium-gated potassium channel.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present(1). In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency(1,2). A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a 'ball-and-chain' mechanism(3-7). Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca(2+), we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca(2+)-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.	+

-	Ball-and-chain inactivation in a calcium-gated potassium channel.,Fan C, Sukomon N, Flood E, Rheinberger J, Allen TW, Nimigean CM Nature. 2020 Apr;580(7802):288-293. doi: 10.1038/s41586-020-2116-0. Epub 2020 Mar, 18. PMID:32269335<ref>PMID:32269335</ref>	+	==See Also==
-		+	*[[Potassium channel 3D structures\|Potassium channel 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6u5p" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fan, C~~]]	+	[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: ~~Nimigean,~~ C M]]	+	[[Category: Fan C]]
-	[[Category: ~~Mthk]]~~	+	[[Category: Nimigean CM]]
-	~~[[Category: Transport protein~~]]	+

OCA at 06:08, 22 April 2020

OCA — Wed, 22 Apr 2020 06:08:54 GMT

←Older revision		Revision as of 06:08, 22 April 2020
Line 3:		Line 3:
	<StructureSection load='6u5p' size='340' side='right'caption='[[6u5p]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6u5p' size='340' side='right'caption='[[6u5p]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u5p]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U5P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6U5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u5p]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U5P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U5P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6u5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u5p OCA], [http://pdbe.org/6u5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u5p RCSB], [http://www.ebi.ac.uk/pdbsum/6u5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u5p ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mthK, MTH_1520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</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=6u5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u5p OCA], [http://pdbe.org/6u5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u5p RCSB], [http://www.ebi.ac.uk/pdbsum/6u5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u5p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MTHK_METTH MTHK_METTH]] Calcium-gated potassium channel.		[[http://www.uniprot.org/uniprot/MTHK_METTH MTHK_METTH]] Calcium-gated potassium channel.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present(1). In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency(1,2). A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a 'ball-and-chain' mechanism(3-7). Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca(2+), we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca(2+)-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.
		+
		+	Ball-and-chain inactivation in a calcium-gated potassium channel.,Fan C, Sukomon N, Flood E, Rheinberger J, Allen TW, Nimigean CM Nature. 2020 Apr;580(7802):288-293. doi: 10.1038/s41586-020-2116-0. Epub 2020 Mar, 18. PMID:32269335<ref>PMID:32269335</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6u5p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:21, 27 March 2020

OCA — Fri, 27 Mar 2020 10:21:23 GMT

←Older revision		Revision as of 10:21, 27 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6u5p is ~~ON HOLD until Paper Publication~~	+	==Calcium-bound MthK gating ring state 1==
-		+	<StructureSection load='6u5p' size='340' side='right'caption='[[6u5p]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6u5p]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U5P FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6u5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u5p OCA], [http://pdbe.org/6u5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u5p RCSB], [http://www.ebi.ac.uk/pdbsum/6u5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u5p ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MTHK_METTH MTHK_METTH]] Calcium-gated potassium channel.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fan, C]]
		+	[[Category: Nimigean, C M]]
		+	[[Category: Mthk]]
		+	[[Category: Transport protein]]

OCA: Protected "6u5p" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 08:15:04 GMT

Protected "6u5p" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:15, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6u5p is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Oct 2019 08:15:02 GMT

New page: '''Unreleased structure''' The entry 6u5p is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6u5p is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]