7ph2 - Revision history

OCA at 16:42, 9 July 2025

2025-07-09T16:42:14Z

← Older revision		Revision as of 16:42, 9 July 2025
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ph2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PH2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ph2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PH2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=88T:(1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione'>88T</scene>, <scene name='pdbligand=EIW:(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{R})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{R})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanylnonanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-oxan-2-yl]methoxy]-5-oxidanyl-oxane-2-carboxylic+acid'>EIW</scene>, <scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</scene></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]] 3.7Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=88T:(1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione'>88T</scene>, <scene name='pdbligand=EIW:(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{R})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{R})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanylnonanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-oxan-2-yl]methoxy]-5-oxidanyl-oxane-2-carboxylic+acid'>EIW</scene>, <scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</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=7ph2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ph2 OCA], [https://pdbe.org/7ph2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ph2 RCSB], [https://www.ebi.ac.uk/pdbsum/7ph2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ph2 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=7ph2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ph2 OCA], [https://pdbe.org/7ph2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ph2 RCSB], [https://www.ebi.ac.uk/pdbsum/7ph2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ph2 ProSAT]</span></td></tr>
	</table>		</table>
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	Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.		Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.

	The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells.,Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA Sci Adv. 2022 Oct 14;8(41):eabn6845. doi: 10.1126/sciadv.abn6845. Epub 2022 Oct, 12. PMID:36223470<ref>PMID:36223470</ref>		The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells.,Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA Sci Adv. 2022 Oct 14;8(41):eabn6845. doi: 10.1126/sciadv.abn6845. Epub 2022 Oct , 12. PMID:36223470<ref>PMID:36223470</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 06:23, 26 October 2022

2022-10-26T06:23:44Z

← Older revision		Revision as of 06:23, 26 October 2022
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	==Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position A60C==		==Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position A60C==
	<StructureSection load='7ph2' size='340' side='right'caption='[[7ph2]]' scene=''>		<StructureSection load='7ph2' size='340' side='right'caption='[[7ph2]], [[Resolution\|resolution]] 3.70Å' 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=7PH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PH2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ph2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PH2 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=7ph2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ph2 OCA], [https://pdbe.org/7ph2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ph2 RCSB], [https://www.ebi.ac.uk/pdbsum/7ph2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ph2 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=88T:(1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione'>88T</scene>, <scene name='pdbligand=EIW:(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{R})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{R})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanylnonanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-oxan-2-yl]methoxy]-5-oxidanyl-oxane-2-carboxylic+acid'>EIW</scene>, <scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</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=7ph2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ph2 OCA], [https://pdbe.org/7ph2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ph2 RCSB], [https://www.ebi.ac.uk/pdbsum/7ph2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ph2 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/MSBA_ECOLI MSBA_ECOLI] Involved in lipid A export and possibly also in glycerophospholipid export and for biogenesis of the outer membrane. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.

			The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells.,Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA Sci Adv. 2022 Oct 14;8(41):eabn6845. doi: 10.1126/sciadv.abn6845. Epub 2022 Oct, 12. PMID:36223470<ref>PMID:36223470</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7ph2" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
			[[Category: Vicugna pacos]]
	[[Category: Bordignon E]]		[[Category: Bordignon E]]
	[[Category: Galazzo L]]		[[Category: Galazzo L]]

OCA at 10:02, 31 August 2022

2022-08-31T10:02:28Z

← Older revision		Revision as of 10:02, 31 August 2022
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	====		==Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position A60C==
	<StructureSection load='7ph2' size='340' side='right'caption='[[7ph2]]' scene=''>		<StructureSection load='7ph2' size='340' side='right'caption='[[7ph2]]' 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'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PH2 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=7ph2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ph2 OCA], [https://pdbe.org/7ph2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ph2 RCSB], [https://www.ebi.ac.uk/pdbsum/7ph2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ph2 ProSAT]</span></td></tr>		</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=7ph2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ph2 OCA], [https://pdbe.org/7ph2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ph2 RCSB], [https://www.ebi.ac.uk/pdbsum/7ph2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ph2 ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Z-disk~~]]		[[Category: Bordignon E]]
			[[Category: Galazzo L]]
			[[Category: Hilbi H]]
			[[Category: Januliene D]]
			[[Category: Kuprov I]]
			[[Category: Meier G]]
			[[Category: Moeller A]]
			[[Category: Parey K]]
			[[Category: Schaefer LV]]
			[[Category: Seeger MA]]
			[[Category: Striednig B]]
			[[Category: Vecchis D]]

OCA at 04:47, 25 August 2022

2022-08-25T04:47:01Z

← Older revision		Revision as of 04:47, 25 August 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7ph2 is ~~ON HOLD until Paper Publication~~		====
			<StructureSection load='7ph2' size='340' side='right'caption='[[7ph2]]' 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=7ph2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ph2 OCA], [https://pdbe.org/7ph2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ph2 RCSB], [https://www.ebi.ac.uk/pdbsum/7ph2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ph2 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Z-disk]]

OCA at 04:45, 9 March 2022

2022-03-09T04:45:51Z

← Older revision		Revision as of 04:45, 9 March 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7ph2 is ON HOLD		The entry 7ph2 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7ph2" [edit=sysop:move=sysop]

2021-08-25T05:12:00Z

Protected "7ph2" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:12, 25 August 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7ph2 is ON HOLD Authors: Description: Category: Unreleased Structures

2021-08-25T05:11:59Z

New page: '''Unreleased structure''' The entry 7ph2 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ph2 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]