4lbe - Revision history

OCA at 10:49, 14 December 2022

OCA — Wed, 14 Dec 2022 10:49:51 GMT

←Older revision		Revision as of 10:49, 14 December 2022
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	==Structure of KcsA with R122A mutation==		==Structure of KcsA with R122A mutation==
-	<StructureSection load='4lbe' size='340' side='right' caption='[[4lbe]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='4lbe' size='340' side='right'caption='[[4lbe]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4lbe]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965~~] and [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LBE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4lbe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LBE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=F09:NONAN-1-OL'>F09</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=F09:NONAN-1-OL'>F09</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lcu\|4lcu]]</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=4lbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lbe OCA], [https://pdbe.org/4lbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lbe RCSB], [https://www.ebi.ac.uk/pdbsum/4lbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lbe ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kcsA, skc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 "Actinomyces lividans" Krasil'nikov et al. 1965])</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=4lbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lbe OCA], [~~http~~://pdbe.org/4lbe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4lbe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4lbe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4lbe ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KCSA_STRLI KCSA_STRLI]] Acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, although it is not clear if this is the physiological stimulus for channel opening. Monovalent cation preference is K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+).<ref>PMID:7489706</ref>	+	[https://www.uniprot.org/uniprot/KCSA_STRLI KCSA_STRLI] Acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, although it is not clear if this is the physiological stimulus for channel opening. Monovalent cation preference is K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+).<ref>PMID:7489706</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4lbe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4lbe" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Potassium channel 3D structures\|Potassium channel 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Actinomyces lividans krasil'nikov et al. 1965~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~McCoy, J M~~]]	+	[[Category: Streptomyces lividans]]
-	[[Category: ~~Nimigean, C M~~]]	+	[[Category: McCoy JM]]
-	[[Category: ~~Posson, D J~~]]	+	[[Category: Nimigean CM]]
-	[[Category: ~~Membrane protein]]~~	+	[[Category: Posson DJ]]
-	~~[[Category: Metal transport]]~~	+
-	~~[[Category: Ph-gated potassium channel]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 06:38, 5 August 2016

OCA — Fri, 05 Aug 2016 06:38:32 GMT

←Older revision		Revision as of 06:38, 5 August 2016
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		+
	==Structure of KcsA with R122A mutation==		==Structure of KcsA with R122A mutation==
	<StructureSection load='4lbe' size='340' side='right' caption='[[4lbe]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='4lbe' size='340' side='right' caption='[[4lbe]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4lbe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LBE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4lbe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=F09:NONAN-1-OL'>F09</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=F09:NONAN-1-OL'>F09</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lcu\|4lcu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lcu\|4lcu]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kcsA, skc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 "Actinomyces lividans" Krasil'nikov et al. 1965])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kcsA, skc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 "Actinomyces lividans" Krasil'nikov et al. 1965])</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=4lbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lbe RCSB], [http://www.ebi.ac.uk/pdbsum/4lbe 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=4lbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lbe OCA], [http://pdbe.org/4lbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lbe RCSB], [http://www.ebi.ac.uk/pdbsum/4lbe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lbe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 4lbe" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Actinomyces lividans krasil'nikov et al. 1965]]		[[Category: Actinomyces lividans krasil'nikov et al. 1965]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: McCoy, J M]]		[[Category: McCoy, J M]]
	[[Category: Nimigean, C M]]		[[Category: Nimigean, C M]]

OCA at 16:35, 25 December 2014

OCA — Thu, 25 Dec 2014 16:35:05 GMT

←Older revision		Revision as of 16:35, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4lbe\| PDB~~=4lbe \| ~~SCENE~~= }}	+	==Structure of KcsA with R122A mutation==
-	===~~Structure of KcsA~~ with ~~R122A mutation~~===	+	<StructureSection load='4lbe' size='340' side='right' caption='[[4lbe]], [[Resolution\|resolution]] 2.75Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24218397}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4lbe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LBE FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=F09:NONAN-1-OL'>F09</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lcu\|4lcu]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kcsA, skc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 "Actinomyces lividans" Krasil'nikov et al. 1965])</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=4lbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lbe RCSB], [http://www.ebi.ac.uk/pdbsum/4lbe PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/KCSA_STRLI KCSA_STRLI]] Acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, although it is not clear if this is the physiological stimulus for channel opening. Monovalent cation preference is K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+).<ref>PMID:7489706</ref>		[[http://www.uniprot.org/uniprot/KCSA_STRLI KCSA_STRLI]] Acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, although it is not clear if this is the physiological stimulus for channel opening. Monovalent cation preference is K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+).<ref>PMID:7489706</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The bacterial potassium channel KcsA is gated open by the binding of protons to amino acids on the intracellular side of the channel. We have identified, via channel mutagenesis and x-ray crystallography, two pH-sensing amino acids and a set of nearby residues involved in molecular interactions that influence gating. We found that the minimal mutation of one histidine (H25) and one glutamate (E118) near the cytoplasmic gate completely abolished pH-dependent gating. Mutation of nearby residues either alone or in pairs altered the channel's response to pH. In addition, mutations of certain pairs of residues dramatically increased the energy barriers between the closed and open states. We proposed a Monod-Wyman-Changeux model for proton binding and pH-dependent gating in KcsA, where H25 is a "strong" sensor displaying a large shift in pKa between closed and open states, and E118 is a "weak" pH sensor. Modifying model parameters that are involved in either the intrinsic gating equilibrium or the pKa values of the pH-sensing residues was sufficient to capture the effects of all mutations.

-	~~==About this Structure==~~	+	Molecular interactions involved in proton-dependent gating in KcsA potassium channels.,Posson DJ, Thompson AN, McCoy JG, Nimigean CM J Gen Physiol. 2013 Dec;142(6):613-24. doi: 10.1085/jgp.201311057. Epub 2013 Nov , 11. PMID:24218397<ref>PMID:24218397</ref>
-	~~[[4lbe]] is a 3 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/"actinomyces_lividans"_krasil'nikov_et_al~~.~~_1965 "actinomyces lividans" krasil'nikov et al~~. ~~1965]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024218397</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Actinomyces lividans krasil'nikov et al. 1965]]		[[Category: Actinomyces lividans krasil'nikov et al. 1965]]
-	[[Category: McCoy, J M.]]	+	[[Category: McCoy, J M]]
-	[[Category: Nimigean, C M.]]	+	[[Category: Nimigean, C M]]
-	[[Category: Posson, D J.]]	+	[[Category: Posson, D J]]
	[[Category: Membrane protein]]		[[Category: Membrane protein]]
	[[Category: Metal transport]]		[[Category: Metal transport]]
	[[Category: Ph-gated potassium channel]]		[[Category: Ph-gated potassium channel]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 07:42, 5 February 2014

OCA — Wed, 05 Feb 2014 07:42:08 GMT

←Older revision		Revision as of 07:42, 5 February 2014
Line 1:		Line 1:
	{{STRUCTURE_4lbe\| PDB=4lbe \| SCENE= }}		{{STRUCTURE_4lbe\| PDB=4lbe \| SCENE= }}
	===Structure of KcsA with R122A mutation===		===Structure of KcsA with R122A mutation===
		+	{{ABSTRACT_PUBMED_24218397}}

	==Function==		==Function==
Line 6:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4lbe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_lividans Streptomyces~~ lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA].	+	[[4lbe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA].

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:024218397</ref><references group="xtra"/><references/>
-	[[Category: ~~Streptomyces~~ lividans]]	+	[[Category: Actinomyces lividans krasil'nikov et al. 1965]]
	[[Category: McCoy, J M.]]		[[Category: McCoy, J M.]]
	[[Category: Nimigean, C M.]]		[[Category: Nimigean, C M.]]

OCA at 09:52, 30 October 2013

OCA — Wed, 30 Oct 2013 09:52:57 GMT

←Older revision		Revision as of 09:52, 30 October 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4lbe\| PDB=4lbe \| SCENE= }}
		+	===Structure of KcsA with R122A mutation===

-	~~The entry 4lbe~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/KCSA_STRLI KCSA_STRLI]] Acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, although it is not clear if this is the physiological stimulus for channel opening. Monovalent cation preference is K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+).<ref>PMID:7489706</ref>

-	~~Authors~~: ~~Nimigean, C~~.M.~~, Posson, D~~.J.~~, McCoy, J~~.M.	+	==About this Structure==
		+	[[4lbe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LBE OCA].

-	~~Description~~: ~~Structure of KcsA with R122A mutation~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Streptomyces lividans]]
		+	[[Category: McCoy, J M.]]
		+	[[Category: Nimigean, C M.]]
		+	[[Category: Posson, D J.]]
		+	[[Category: Membrane protein]]
		+	[[Category: Metal transport]]
		+	[[Category: Ph-gated potassium channel]]
		+	[[Category: Transport protein]]

OCA at 07:15, 14 August 2013

OCA — Wed, 14 Aug 2013 07:15:36 GMT

←Older revision		Revision as of 07:15, 14 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4lbe is ON HOLD	+	The entry 4lbe is ON HOLD until Paper Publication

	Authors: Nimigean, C.M., Posson, D.J., McCoy, J.M.		Authors: Nimigean, C.M., Posson, D.J., McCoy, J.M.

-	Description: ~~pH Sensing Mutants~~ of KcsA	+	Description: Structure of KcsA with R122A mutation

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

OCA — Sun, 30 Jun 2013 09:12:52 GMT

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

←Older revision

Revision as of 09:12, 30 June 2013

OCA: New page: '''Unreleased structure''' The entry 4lbe is ON HOLD Authors: Nimigean, C.M., Posson, D.J., McCoy, J.M. Description: pH Sensing Mutants of KcsA

OCA — Sun, 30 Jun 2013 09:12:49 GMT

New page: '''Unreleased structure''' The entry 4lbe is ON HOLD Authors: Nimigean, C.M., Posson, D.J., McCoy, J.M. Description: pH Sensing Mutants of KcsA

New page

'''Unreleased structure'''

The entry 4lbe is ON HOLD

Authors: Nimigean, C.M., Posson, D.J., McCoy, J.M.

Description: pH Sensing Mutants of KcsA