OCA at 14:08, 18 October 2023

OCA — Wed, 18 Oct 2023 14:08:29 GMT

←Older revision		Revision as of 14:08, 18 October 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8ijl is ~~ON HOLD until Paper~~ Publication	+	==Cyo-EM structure of wildtype non-gastric proton pump in the presence of Na+, AlF and ADP==
		+	<StructureSection load='8ijl' size='340' side='right'caption='[[8ijl]], [[Resolution\|resolution]] 2.62Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8ijl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus Rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IJL FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 2.62Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=Q7G:2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl+4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside'>Q7G</scene></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=8ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ijl OCA], [https://pdbe.org/8ijl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ijl RCSB], [https://www.ebi.ac.uk/pdbsum/8ijl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ijl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G3V8S4_RAT G3V8S4_RAT]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Na(+),K(+)-ATPase (NKA) and non-gastric H(+),K(+)- ATPase (ngHKA) share ~65 % sequence identity, and nearly identical catalytic cycles. These pumps alternate between inward-facing (E1) and outward-facing (E2) conformations and differ in their exported substrate (Na(+) or H(+)) and stoichiometries (3 Na(+):2 K(+) or 1 H(+):1 K(+)). We reported that structures of the NKA-mimetic ngHKA mutant K794S/A797P/W940/R949C (SPWC) with 2 K(+) occluded in E2-P(i) and 3 Na(+)-bound in E1.ATP states were nearly identical to NKA structures in equivalent states. Here we report the cryo-EM structures of K794A and K794S, two poorly-selective ngHKA mutants, under conditions to stabilize the E1.ATP state. Unexpectedly, the structures show a hybrid with both E1- and E2-like structural features. While transmembrane segments TM1-TM3 and TM4's extracellular half adopted an E2-like conformation, the rest of the protein assumed an E1 configuration. Two spherical densities, likely bound Na(+), were observed at cation-binding sites I and III, without density at site II. This explains the E2-like conformation of TM4's exoplasmic half. In NKA, oxygen atoms derived from the unwound portion of TM4 coordinated Na(+) at site II. Thus, the lack of Na(+) at site II of K794A/S prevents the luminal portion of TM4 from taking an E1-like position. The K794A structure also suggests that incomplete coordination of Na(+) at site III induces the halfway rotation of TM6, which impairs Na(+)-binding at the site II. Thus, our observations provide insight into the molecular mechanism of E2-E1 transition and cooperative Na(+)-binding in the NKA and other related cation pumps.

-	~~Authors~~:	+	An unusual conformation from Na(+)-sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na(+)-binding.,Abe K, Nishizawa T, Artigas P Biochim Biophys Acta Mol Cell Res. 2023 Oct;1870(7):119543. doi: , 10.1016/j.bbamcr.2023.119543. Epub 2023 Jul 22. PMID:37482134<ref>PMID:37482134</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8ijl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rattus]]
		+	[[Category: Abe K]]

OCA at 08:07, 15 March 2023

OCA — Wed, 15 Mar 2023 08:07:21 GMT

←Older revision		Revision as of 08:07, 15 March 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8ijl is ON HOLD	+	The entry 8ijl is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8ijl" [edit=sysop:move=sysop]

OCA — Wed, 08 Mar 2023 05:55:02 GMT

Protected "8ijl" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:55, 8 March 2023

OCA: New page: '''Unreleased structure''' The entry 8ijl is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Mar 2023 05:55:01 GMT

New page: '''Unreleased structure''' The entry 8ijl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8ijl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

8ijl - Revision history

OCA at 14:08, 18 October 2023

OCA at 08:07, 15 March 2023

OCA: Protected "8ijl" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8ijl is ON HOLD Authors: Description: Category: Unreleased Structures