6jxj - Revision history

OCA at 10:21, 22 November 2023

OCA — Wed, 22 Nov 2023 10:21:29 GMT

←Older revision		Revision as of 10:21, 22 November 2023
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	<StructureSection load='6jxj' size='340' side='right'caption='[[6jxj]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6jxj' size='340' side='right'caption='[[6jxj]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jxj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jxj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JXJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</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]] 2.5Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATP4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), ATP4B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)/K(+)-exchanging_ATPase H(+)/K(+)-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.2.2.19 7.2.2.19] </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=6jxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxj OCA], [https://pdbe.org/6jxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jxj RCSB], [https://www.ebi.ac.uk/pdbsum/6jxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxj 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=6jxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxj OCA], [~~http~~://pdbe.org/6jxj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jxj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jxj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxj ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/ATP4B_PIG ATP4B_PIG]] Note=Parietal cell autoantigen associated with autoimmune gastritis.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.	+	[https://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 30:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pig~~]]	+	[[Category: Sus scrofa]]
-	[[Category: Abe, K]]	+	[[Category: Abe K]]
-	[[Category: Irie, K]]	+	[[Category: Irie K]]
-	~~[[Category: Gastric]]~~	+
-	~~[[Category: Ion pump]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: P-type atpase]]~~	+
-	~~[[Category: Proton pump~~]]	+

OCA at 07:19, 30 September 2020

OCA — Wed, 30 Sep 2020 07:19:44 GMT

←Older revision		Revision as of 07:19, 30 September 2020
Line 3:		Line 3:
	<StructureSection load='6jxj' size='340' side='right'caption='[[6jxj]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6jxj' size='340' side='right'caption='[[6jxj]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jxj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jxj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JXJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATP4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), ATP4B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)/K(+)-exchanging_ATPase H(+)/K(+)-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.2.2.19 7.2.2.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)/K(+)-exchanging_ATPase H(+)/K(+)-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.2.2.19 7.2.2.19] </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=6jxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxj OCA], [http://pdbe.org/6jxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxj RCSB], [http://www.ebi.ac.uk/pdbsum/6jxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxj 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=6jxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxj OCA], [http://pdbe.org/6jxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxj RCSB], [http://www.ebi.ac.uk/pdbsum/6jxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxj ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 12:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.		[[http://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The gastric proton pump (H(+),K(+)-ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H(+) and K(+) coupled with ATP hydrolysis, but with an as yet undetermined transport stoichiometry. Here we show crystal structures at a resolution of 2.5 A of the pump in the E2-P transition state, in which the counter-transporting cation is occluded. We found a single K(+) bound to the cation-binding site of the H(+),K(+)-ATPase, indicating an exchange of 1H(+)/1K(+) per hydrolysis of one ATP molecule. This fulfills the energy requirement for the generation of a six pH unit gradient across the membrane. The structural basis of K(+) recognition is resolved and supported by molecular dynamics simulations, establishing how the H(+),K(+)-ATPase overcomes the energetic challenge to generate an H(+) gradient of more than a million-fold-one of the highest cation gradients known in mammalian tissue-across the membrane.
		+
		+	A single K(+)-binding site in the crystal structure of the gastric proton pump.,Yamamoto K, Dubey V, Irie K, Nakanishi H, Khandelia H, Fujiyoshi Y, Abe K Elife. 2019 Aug 22;8. pii: 47701. doi: 10.7554/eLife.47701. PMID:31436534<ref>PMID:31436534</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jxj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ATPase 3D structures\|ATPase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pig]]
	[[Category: Abe, K]]		[[Category: Abe, K]]
	[[Category: Irie, K]]		[[Category: Irie, K]]

OCA at 16:34, 14 August 2019

OCA — Wed, 14 Aug 2019 16:34:27 GMT

←Older revision		Revision as of 16:34, 14 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jxj ~~is ON HOLD until Paper Publication~~	+	==Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp)==
-		+	<StructureSection load='6jxj' size='340' side='right'caption='[[6jxj]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~: ~~Abe, K~~., ~~Irie~~, K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jxj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JXJ FirstGlance]. <br>
-	~~Description~~: ~~Rb+~~-~~bound E2~~-~~AlF state~~ of the ~~gastric proton pump~~ (~~Tyr799Trp~~)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)/K(+)-exchanging_ATPase H(+)/K(+)-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.2.2.19 7.2.2.19] </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=6jxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxj OCA], [http://pdbe.org/6jxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxj RCSB], [http://www.ebi.ac.uk/pdbsum/6jxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxj ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ATP4B_PIG ATP4B_PIG]] Note=Parietal cell autoantigen associated with autoimmune gastritis.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Abe, K]]
	[[Category: Irie, K]]		[[Category: Irie, K]]
-	[[Category: ~~Abe, K~~]]	+	[[Category: Gastric]]
		+	[[Category: Ion pump]]
		+	[[Category: Membrane protein]]
		+	[[Category: P-type atpase]]
		+	[[Category: Proton pump]]

OCA at 05:36, 21 May 2019

OCA — Tue, 21 May 2019 05:36:35 GMT

←Older revision		Revision as of 05:36, 21 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Abe, K., Irie, K.		Authors: Abe, K., Irie, K.

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

OCA — Wed, 01 May 2019 07:00:04 GMT

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

←Older revision

Revision as of 07:00, 1 May 2019

OCA: New page: '''Unreleased structure''' The entry 6jxj is ON HOLD Authors: Abe, K., Irie, K. Description: Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp) [[Category: Unreleased Struct...

OCA — Wed, 01 May 2019 07:00:02 GMT

New page: '''Unreleased structure''' The entry 6jxj is ON HOLD Authors: Abe, K., Irie, K. Description: Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp) [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 6jxj is ON HOLD

Authors: Abe, K., Irie, K.

Description: Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp)
[[Category: Unreleased Structures]]
[[Category: Irie, K]]
[[Category: Abe, K]]