OCA at 19:30, 29 May 2024

OCA — Wed, 29 May 2024 19:30:59 GMT

←Older revision		Revision as of 19:30, 29 May 2024
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-	====	+	==2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane==
-	<StructureSection load='7cub' size='340' side='right'caption='[[7cub]]' scene=''>	+	<StructureSection load='7cub' size='340' side='right'caption='[[7cub]], [[Resolution\|resolution]] 2.55Å' 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'>[[7cub]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CUB 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=7cub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cub OCA], [https://pdbe.org/7cub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cub RCSB], [https://www.ebi.ac.uk/pdbsum/7cub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cub ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 2.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HEO:HEME+O'>HEO</scene>, <scene name='pdbligand=UQ8:UBIQUINONE-8'>UQ8</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=7cub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cub OCA], [https://pdbe.org/7cub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cub RCSB], [https://www.ebi.ac.uk/pdbsum/7cub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cub ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CYOB_ECOLI CYOB_ECOLI] Cytochrome bo(3) ubiquinol terminal oxidase is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at high aeration. Has proton pump activity across the membrane in addition to electron transfer, pumping 2 protons/electron. Protons are probably pumped via D- and K- channels found in this subunit (PubMed:11017202).<ref>PMID:6308657</ref> <ref>PMID:19542282</ref> <ref>PMID:22843529</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two independent structures of the proton-pumping, respiratory cytochrome bo(3) ubiquinol oxidase (cyt bo(3) ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-A resolution, respectively. The structures include the metal redox centers (heme b, heme o(3) , and Cu(B)), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75(I) and R71(I) In both structures, residue H98(I) occupies two conformations. In conformation 1, H98(I) forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98(I) has flipped to form a hydrogen bond with E14(I) at the N-terminal end of TM0. We propose that H98(I) dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98(I).
		+
		+	Cryo-EM structures of Escherichia coli cytochrome bo(3) reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.,Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R Proc Natl Acad Sci U S A. 2021 Aug 24;118(34):e2106750118. doi: , 10.1073/pnas.2106750118. PMID:34417297<ref>PMID:34417297</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7cub" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Gennis RB]]
		+	[[Category: Han L]]
		+	[[Category: Li J]]
		+	[[Category: Zhang K]]
		+	[[Category: Zhu JP]]

OCA at 06:17, 25 August 2021

OCA — Wed, 25 Aug 2021 06:17:49 GMT

←Older revision		Revision as of 06:17, 25 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7cub ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7cub' size='340' side='right'caption='[[7cub]]' scene=''>
-	~~Authors~~:	+	== 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~~:	+	</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=7cub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cub OCA], [https://pdbe.org/7cub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cub RCSB], [https://www.ebi.ac.uk/pdbsum/7cub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cub ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 07:43, 21 July 2021

OCA — Wed, 21 Jul 2021 07:43:45 GMT

←Older revision		Revision as of 07:43, 21 July 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7cub is ON HOLD	+	The entry 7cub is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 08:37, 14 July 2021

OCA — Wed, 14 Jul 2021 08:37:43 GMT

←Older revision		Revision as of 08:37, 14 July 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7cub is ON HOLD ~~until Paper Publication~~	+	The entry 7cub is ON HOLD

	Authors:		Authors:

OCA at 05:28, 24 February 2021

OCA — Wed, 24 Feb 2021 05:28:12 GMT

←Older revision		Revision as of 05:28, 24 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7cub is ON HOLD	+	The entry 7cub is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 02 Sep 2020 05:12:30 GMT

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

←Older revision

Revision as of 05:12, 2 September 2020

OCA: New page: '''Unreleased structure''' The entry 7cub is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Sep 2020 05:12:29 GMT

New page: '''Unreleased structure''' The entry 7cub is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7cub is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]