5ksd - Revision history

OCA at 10:52, 27 September 2023

2023-09-27T10:52:58Z

←Older revision		Revision as of 10:52, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5ksd' size='340' side='right'caption='[[5ksd]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5ksd' size='340' side='right'caption='[[5ksd]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ksd]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3b8c 3b8c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KSD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ksd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3b8c 3b8c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KSD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.5Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AHA2, At4g30190, F9N11.40 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proton-exporting_ATPase Proton-exporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.6 3.6.3.6] </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=5ksd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ksd OCA], [https://pdbe.org/5ksd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ksd RCSB], [https://www.ebi.ac.uk/pdbsum/5ksd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ksd ProSAT]</span></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=5ksd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ksd OCA], [~~http~~://pdbe.org/5ksd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ksd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ksd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ksd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PMA2_ARATH PMA2_ARATH]] The plasma membrane H(+) ATPase of plants and fungi generates a proton gradient that drives the active transport of nutrients by H(+)-symport. The resulting external acidification and/or internal alkinization may mediate growth responses.	+	[https://www.uniprot.org/uniprot/PMA2_ARATH PMA2_ARATH] The plasma membrane H(+) ATPase of plants and fungi generates a proton gradient that drives the active transport of nutrients by H(+)-symport. The resulting external acidification and/or internal alkinization may mediate growth responses.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Proton-exporting ATPase]]~~	+	[[Category: Croll T]]
-	[[Category: Croll, T]]	+	[[Category: Nissen P]]
-	[[Category: Nissen, P]]	+	[[Category: Pedersen BP]]
-	[[Category: Pedersen~~, B P]]~~	+
-	~~[[Category: P-type atpase proton transport]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 06:33, 5 August 2020

2020-08-05T06:33:25Z

←Older revision		Revision as of 06:33, 5 August 2020
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	==Crystal Structure of a Plasma Membrane Proton Pump==		==Crystal Structure of a Plasma Membrane Proton Pump==
-	<StructureSection load='5ksd' size='340' side='right' caption='[[5ksd]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5ksd' size='340' side='right'caption='[[5ksd]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ksd]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3b8c 3b8c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KSD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ksd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3b8c 3b8c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KSD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AHA2, At4g30190, F9N11.40 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proton-exporting_ATPase Proton-exporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.6 3.6.3.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proton-exporting_ATPase Proton-exporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.6 3.6.3.6] </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=5ksd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ksd OCA], [http://pdbe.org/5ksd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ksd RCSB], [http://www.ebi.ac.uk/pdbsum/5ksd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ksd ProSAT]</span></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=5ksd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ksd OCA], [http://pdbe.org/5ksd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ksd RCSB], [http://www.ebi.ac.uk/pdbsum/5ksd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ksd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:

	==See Also==		==See Also==
-	*[[ATPase\|ATPase]]	+	*[[ATPase 3D structures\|ATPase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Proton-exporting ATPase]]		[[Category: Proton-exporting ATPase]]
	[[Category: Croll, T]]		[[Category: Croll, T]]

OCA at 06:18, 10 May 2017

2017-05-10T06:18:20Z

←Older revision		Revision as of 06:18, 10 May 2017
Line 12:		Line 12:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~A prerequisite for life is the ability to maintain electrochemical imbalances across biomembranes. In all eukaryotes the~~ plasma membrane ~~potential and secondary transport systems are energized by the activity of P-type ATPase membrane proteins:~~ H+-ATPase ~~(the~~ proton pump) in plants and fungi, and ~~Na+~~,K+-ATPase (~~the sodium-potassium pump~~) in ~~animals~~. ~~The name P-type derives from the fact that these proteins exploit~~ a ~~phosphorylated reaction cycle intermediate~~ of ~~ATP hydrolysis. The plasma membrane proton pumps belong to~~ the ~~type III P~~-~~type ATPase subfamily~~, ~~whereas Na+~~,K+-~~ATPase~~ and Ca2+-ATPase ~~are type II. Electron microscopy has revealed the overall shape~~ of proton ~~pumps, however, an atomic structure has been lacking. Here we present the first structure~~ of a P-type ~~proton pump determined by X~~-~~ray crystallography~~. ~~Ten transmembrane helices~~ and ~~three cytoplasmic domains define the functional unit~~ of ~~ATP-coupled proton transport across~~ the ~~plasma membrane~~, ~~and~~ the ~~structure~~ is ~~locked~~ in a ~~functional state not previously observed~~ in P-~~type ATPases. The transmembrane domain reveals a large cavity~~, which ~~is likely to be filled~~ with ~~water, located near~~ the ~~middle of the membrane plane where it is lined by conserved hydrophilic and charged residues. Proton transport against a high membrane potential is readily explained by this structural arrangement~~.	+	The plasma membrane H+-ATPase is a proton pump of the P-type ATPase family and essential in plants and fungi. It extrudes protons to regulate pH and maintains a strong proton-motive force that energizes e.g., secondary uptake of nutrients. The only crystal structure of a H+-ATPase (AHA2 from Arabidopsis thaliana) was reported in 2007. Here, we present an improved atomic model of AHA2, obtained by a combination of model rebuilding through interactive molecular dynamics flexible fitting (iMDFF) and structural refinement based on the original data, but using up-to-date refinement methods. More detailed map features prompted local corrections of the transmembrane domain, in particular rearrangement of transmembrane helices 7 and 8, and the cytoplasmic N- and P-domains, and the new model shows improved overall quality and reliability scores. The AHA2 structure shows similarity to the Ca2+-ATPase E1 state, and provides a valuable starting point model for structural and functional analysis of proton transport mechanism of P-type H+-ATPases. Specifically, Asp684 protonation associated with phosphorylation and occlusion of the E1P state may result from hydrogen bond interaction with Asn106. A subsequent deprotonation associated with extracellular release in the E2P state may result from an internal salt bridge formation to an Arg655 residue, which in the present E1 state is stabilized in a solvated pocket. A release mechanism based on an in-built counter-cation was also later proposed for Zn2+-ATPase, for which structures have been determined in Zn2+ released E2P-like states with the salt bridge interaction formed.

-	~~Crystal structure~~ of the ~~plasma membrane proton pump~~.,Pedersen BP~~, Buch-Pedersen MJ, Morth JP, Palmgren MG~~, Nissen P ~~Nature~~. ~~2007 Dec 13~~;~~450(7172)~~:~~1111-4~~. PMID:~~18075595~~<ref>PMID:~~18075595~~</ref>	+	Improved Model of Proton Pump Crystal Structure Obtained by Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model for Proton Translocation in P-Type ATPases.,Focht D, Croll TI, Pedersen BP, Nissen P Front Physiol. 2017 Apr 11;8:202. doi: 10.3389/fphys.2017.00202. eCollection, 2017. PMID:28443028<ref>PMID:28443028</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>
	</div>		</div>
	<div class="pdbe-citations 5ksd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ksd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ATPase\|ATPase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:48, 10 August 2016

2016-08-10T15:48:29Z

←Older revision		Revision as of 15:48, 10 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The~~ entry 5ksd is ~~ON HOLD~~	+	==Crystal Structure of a Plasma Membrane Proton Pump==
		+	<StructureSection load='5ksd' size='340' side='right' caption='[[5ksd]], [[Resolution\|resolution]] 3.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ksd]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3b8c 3b8c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KSD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proton-exporting_ATPase Proton-exporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.6 3.6.3.6] </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=5ksd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ksd OCA], [http://pdbe.org/5ksd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ksd RCSB], [http://www.ebi.ac.uk/pdbsum/5ksd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ksd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PMA2_ARATH PMA2_ARATH]] The plasma membrane H(+) ATPase of plants and fungi generates a proton gradient that drives the active transport of nutrients by H(+)-symport. The resulting external acidification and/or internal alkinization may mediate growth responses.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A prerequisite for life is the ability to maintain electrochemical imbalances across biomembranes. In all eukaryotes the plasma membrane potential and secondary transport systems are energized by the activity of P-type ATPase membrane proteins: H+-ATPase (the proton pump) in plants and fungi, and Na+,K+-ATPase (the sodium-potassium pump) in animals. The name P-type derives from the fact that these proteins exploit a phosphorylated reaction cycle intermediate of ATP hydrolysis. The plasma membrane proton pumps belong to the type III P-type ATPase subfamily, whereas Na+,K+-ATPase and Ca2+-ATPase are type II. Electron microscopy has revealed the overall shape of proton pumps, however, an atomic structure has been lacking. Here we present the first structure of a P-type proton pump determined by X-ray crystallography. Ten transmembrane helices and three cytoplasmic domains define the functional unit of ATP-coupled proton transport across the plasma membrane, and the structure is locked in a functional state not previously observed in P-type ATPases. The transmembrane domain reveals a large cavity, which is likely to be filled with water, located near the middle of the membrane plane where it is lined by conserved hydrophilic and charged residues. Proton transport against a high membrane potential is readily explained by this structural arrangement.

-	~~Authors: Croll, T~~., Pedersen, ~~B.P.~~, ~~Nissen~~, P.	+	Crystal structure of the plasma membrane proton pump.,Pedersen BP, Buch-Pedersen MJ, Morth JP, Palmgren MG, Nissen P Nature. 2007 Dec 13;450(7172):1111-4. PMID:18075595<ref>PMID:18075595</ref>

-	~~Description: Crystal Structure~~ of ~~a Plasma Membrane Proton Pump~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Nissen, P]]~~	+	<div class="pdbe-citations 5ksd" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Pedersen, B.P~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Proton-exporting ATPase]]
	[[Category: Croll, T]]		[[Category: Croll, T]]
		+	[[Category: Nissen, P]]
		+	[[Category: Pedersen, B P]]
		+	[[Category: P-type atpase proton transport]]
		+	[[Category: Transport protein]]

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

2016-07-26T12:48:21Z

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

←Older revision

Revision as of 12:48, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ksd is ON HOLD Authors: Croll, T., Pedersen, B.P., Nissen, P. Description: Crystal Structure of a Plasma Membrane Proton Pump [[Category: Unreleas...

2016-07-26T12:48:20Z

New page: '''Unreleased structure''' The entry 5ksd is ON HOLD Authors: Croll, T., Pedersen, B.P., Nissen, P. Description: Crystal Structure of a Plasma Membrane Proton Pump [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5ksd is ON HOLD

Authors: Croll, T., Pedersen, B.P., Nissen, P.

Description: Crystal Structure of a Plasma Membrane Proton Pump
[[Category: Unreleased Structures]]
[[Category: Nissen, P]]
[[Category: Pedersen, B.P]]
[[Category: Croll, T]]