7xk7 - Revision history

OCA at 05:03, 8 September 2022

OCA — Thu, 08 Sep 2022 05:03:07 GMT

←Older revision		Revision as of 05:03, 8 September 2022
Line 1:		Line 1:

-	====	+	==Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with korormicin==
-	<StructureSection load='7xk7' size='340' side='right'caption='[[7xk7]]' scene=''>	+	<StructureSection load='7xk7' size='340' side='right'caption='[[7xk7]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7xk7]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O395 Vibrio cholerae O395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XK7 FirstGlance]. <br>
-	</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=7xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xk7 OCA], [https://pdbe.org/7xk7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xk7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xk7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xk7 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IQT:Korormicin'>IQT</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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=7xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xk7 OCA], [https://pdbe.org/7xk7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xk7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xk7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xk7 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/NQRA_VIBC3 NQRA_VIBC3]] NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol.[HAMAP-Rule:MF_00425]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Na(+)-pumping NADH-ubiquinone oxidoreductase (Na(+)-NQR) couples electron transfer from NADH to ubiquinone with Na(+)-pumping, generating an electrochemical Na(+) gradient that is essential for energy-consuming reactions in bacteria. Since Na(+)-NQR is exclusively found in prokaryotes, it is a promising target for highly selective antibiotics. However, the molecular mechanism of inhibition is not well-understood for lack of the atomic structural information about an inhibitor-bound state. Here we present cryo-electron microscopy structures of Na(+)-NQR from Vibrio cholerae with or without a bound inhibitor at 2.5- to 3.1-A resolution. The structures reveal the arrangement of all six redox cofactors including a herein identified 2Fe-2S cluster located between the NqrD and NqrE subunits. A large part of the hydrophilic NqrF is barely visible in the density map, suggesting a high degree of flexibility. This flexibility may be responsible to reducing the long distance between the 2Fe-2S centers in NqrF and NqrD/E. Two different types of specific inhibitors bind to the N-terminal region of NqrB, which is disordered in the absence of inhibitors. The present study provides a foundation for understanding the function of Na(+)-NQR and the binding manner of specific inhibitors.
		+
		+	Cryo-EM structures of Na(+)-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae.,Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H Nat Commun. 2022 Jul 26;13(1):4082. doi: 10.1038/s41467-022-31718-1. PMID:35882843<ref>PMID:35882843</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7xk7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Vibrio cholerae O395]]
		+	[[Category: Barquera B]]
		+	[[Category: Ishikawa M]]
		+	[[Category: Kishikawa J]]
		+	[[Category: Masuya T]]
		+	[[Category: Miyoshi H]]
		+	[[Category: Murai M]]

OCA at 06:56, 20 July 2022

OCA — Wed, 20 Jul 2022 06:56:05 GMT

←Older revision		Revision as of 06:56, 20 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7xk7 ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7xk7' size='340' side='right'caption='[[7xk7]]' scene=''>
-	~~Authors~~: ~~Kishikawa, J~~.~~, Ishikawa, M~~.~~, Masuya, T~~.~~, Murai, M~~.~~, Barquera, B~~.~~, Miyoshi, H~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with korormicin~~	+	</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=7xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xk7 OCA], [https://pdbe.org/7xk7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xk7 RCSB], [https://www.ebi.ac.uk/pdbsum/7xk7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xk7 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Barquera, B~~]]	+	__TOC__
-	[~~[Category~~: ~~Ishikawa, M~~]]	+	</StructureSection>
-	[~~[Category~~: ~~Kishikawa, J~~]]	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Miyoshi~~, H]]	+	[[Category: Z-disk]]
-	[[Category: ~~Masuya, T~~]]	+
-	[[Category: ~~Murai, M~~]]	+

OCA: Protected "7xk7" [edit=sysop:move=sysop]

OCA — Wed, 27 Apr 2022 10:34:16 GMT

Protected "7xk7" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:34, 27 April 2022

OCA: New page: '''Unreleased structure''' The entry 7xk7 is ON HOLD Authors: Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H. Description: Cryo-EM structure of Na+-pumpin...

OCA — Wed, 27 Apr 2022 10:34:15 GMT

New page: '''Unreleased structure''' The entry 7xk7 is ON HOLD Authors: Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H. Description: Cryo-EM structure of Na+-pumpin...

New page

'''Unreleased structure'''

The entry 7xk7 is ON HOLD

Authors: Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Barquera, B., Miyoshi, H.

Description: Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with korormicin
[[Category: Unreleased Structures]]
[[Category: Barquera, B]]
[[Category: Ishikawa, M]]
[[Category: Kishikawa, J]]
[[Category: Miyoshi, H]]
[[Category: Masuya, T]]
[[Category: Murai, M]]