7yzr - Revision history

OCA at 13:27, 1 February 2024

OCA — Thu, 01 Feb 2024 13:27:50 GMT

←Older revision		Revision as of 13:27, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7yzr]] is a 6 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=7YZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZR FirstGlance]. <br>		<table><tr><td colspan='2'>[[7yzr]] is a 6 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=7YZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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]] 6.92Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7yzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzr OCA], [https://pdbe.org/7yzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzr RCSB], [https://www.ebi.ac.uk/pdbsum/7yzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzr 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=7yzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzr OCA], [https://pdbe.org/7yzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzr RCSB], [https://www.ebi.ac.uk/pdbsum/7yzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzr ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:10, 24 November 2022

OCA — Thu, 24 Nov 2022 10:10:48 GMT

←Older revision		Revision as of 10:10, 24 November 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7yzr is ~~ON HOLD~~	+	==50 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-BeFx (rigid body model)==
		+	<StructureSection load='7yzr' size='340' side='right'caption='[[7yzr]], [[Resolution\|resolution]] 6.92Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7yzr]] is a 6 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=7YZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7yzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzr OCA], [https://pdbe.org/7yzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzr RCSB], [https://www.ebi.ac.uk/pdbsum/7yzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzr ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AT1A1_PIG AT1A1_PIG] This is the catalytic component of the active enzyme, which catalyzes the hydrolysis of ATP coupled with the exchange of sodium and potassium ions across the plasma membrane. This action creates the electrochemical gradient of sodium and potassium ions, providing the energy for active transport of various nutrients.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Na(+),K(+)-ATPase generates electrochemical gradients of Na(+) and K(+) across the plasma membrane via a functional cycle that includes various phosphoenzyme intermediates. However, the structure and function of these intermediates and how metal fluorides mimick them require further investigation. Here, we describe a 4.0 A resolution crystal structure and functional properties of the pig kidney Na(+),K(+)-ATPase stabilized by the inhibitor beryllium fluoride (denoted E2-BeF(x)). E2-BeF(x) is expected to mimic properties of the E2P phosphoenzyme, yet with unknown characteristics of ion and ligand binding. The structure resembles the E2P form obtained by phosphorylation from inorganic phosphate (P(i)) and stabilized by cardiotonic steroids, including a low-affinity Mg(2+) site near ion binding site II. Our anomalous Fourier analysis of the crystals soaked in Rb(+) (a K(+) congener) followed by a low-resolution rigid-body refinement (6.9-7.5 A) revealed preocclusion transitions leading to activation of the dephosphorylation reaction. We show that the Mg(2+) location indicates a site of initial K(+) recognition and acceptance upon binding to the outward-open E2P state after Na(+) release. Furthermore, using binding and activity studies, we find that the BeF(x)-inhibited enzyme is also able to bind ADP/ATP and Na(+). These results relate the E2-BeF(x) complex to a transient K(+)- and ADP-sensitive E *P intermediate of the functional cycle of the Na(+),K(+)-ATPase, prior to E2P.

-	~~Authors: Fruergaard~~, ~~M.U~~., Dach, I., Andersen~~, J.L.~~, Ozol, M~~., Shasavar~~, A., Quistgaard~~, E.M.~~, Poulsen, H., Fedosova, N.U., ~~Nissen, P~~.	+	The Na(+),K(+)-ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state.,Fruergaard MU, Dach I, Andersen JL, Ozol M, Shahsavar A, Quistgaard EM, Poulsen H, Fedosova NU, Nissen P J Biol Chem. 2022 Sep;298(9):102317. doi: 10.1016/j.jbc.2022.102317. Epub 2022 , Aug 2. PMID:35926706<ref>PMID:35926706</ref>

-	~~Description: 50 mM Rb+ soak of beryllium fluoride inhibited Na+~~,K+-~~ATPase, E2~~-~~BeFx (rigid body model)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Andersen~~, J.L~~]]	+	<div class="pdbe-citations 7yzr" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Shasavar, A~~]]	+	== References ==
-	[[Category: ~~Ozol, M~~]]	+	<references/>
-	[[Category: Fruergaard~~, M.U~~]]	+	__TOC__
-	[[Category: Nissen, P]]	+	</StructureSection>
-	[[Category: ~~Fedosova, N.U~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Dach, I~~]]	+	[[Category: Sus scrofa]]
-	[[Category: Quistgaard~~, E.M~~]]	+	[[Category: Andersen JL]]
-	[[Category: ~~Poulsen, H~~]]	+	[[Category: Dach I]]
		+	[[Category: Fedosova NU]]
		+	[[Category: Fruergaard MU]]
		+	[[Category: Nissen P]]
		+	[[Category: Ozol M]]
		+	[[Category: Poulsen H]]
		+	[[Category: Quistgaard EM]]
		+	[[Category: Shasavar A]]

OCA: Protected "7yzr" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2022 05:20:38 GMT

Protected "7yzr" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:20, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7yzr is ON HOLD Authors: Fruergaard, M.U., Dach, I., Andersen, J.L., Ozol, M., Shasavar, A., Quistgaard, E.M., Poulsen, H., Fedosova, N.U., Nissen, ...

OCA — Wed, 02 Mar 2022 05:20:38 GMT

New page: '''Unreleased structure''' The entry 7yzr is ON HOLD Authors: Fruergaard, M.U., Dach, I., Andersen, J.L., Ozol, M., Shasavar, A., Quistgaard, E.M., Poulsen, H., Fedosova, N.U., Nissen, ...

New page

'''Unreleased structure'''

The entry 7yzr is ON HOLD

Authors: Fruergaard, M.U., Dach, I., Andersen, J.L., Ozol, M., Shasavar, A., Quistgaard, E.M., Poulsen, H., Fedosova, N.U., Nissen, P.

Description: 50 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-BeFx (rigid body model)
[[Category: Unreleased Structures]]
[[Category: Andersen, J.L]]
[[Category: Shasavar, A]]
[[Category: Ozol, M]]
[[Category: Fruergaard, M.U]]
[[Category: Nissen, P]]
[[Category: Fedosova, N.U]]
[[Category: Dach, I]]
[[Category: Quistgaard, E.M]]
[[Category: Poulsen, H]]