6ye4 - Revision history

OCA at 12:59, 4 May 2022

OCA — Wed, 04 May 2022 12:59:06 GMT

←Older revision		Revision as of 12:59, 4 May 2022
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for~~ the ~~refinement~~ of ~~macromolecular structures by single~~-~~particle analysis of electron cryo~~-~~microscopy~~ (~~cryo~~-EM) ~~data~~. ~~Whereas alternative approaches often rely on user expertise for the tuning~~ of ~~parameters~~, ~~RELION uses~~ a ~~Bayesian approach to infer parameters~~ of ~~a statistical model from the data~~. ~~This paper describes developments that reduce~~ the ~~computational costs~~ of the ~~underlying maximum~~ a ~~posteriori (MAP) algorithm~~, ~~as well as statistical considerations~~ that ~~yield new insights into the accuracy~~ with ~~which~~ the ~~relative orientations~~ of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and ~~reliable resolution estimates~~ with ~~minimal user intervention~~ and ~~at acceptable computational costs~~.	+	ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbBSm has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbB's are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbBSm and HasB. We determined the cryo-EM structures of ExbBSm and of the ExbB-ExbDSm complex from S. marcescens. ExbBSm alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbBSm extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbBSm and ExbBEc, essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the class of inner membrane energy machinery formed by ExbB, ExbD and HasB.

-	~~RELION: implementation~~ of a ~~Bayesian approach to cryo-EM structure determination~~.,~~Scheres SH~~ J ~~Struct~~ Biol. ~~2012 Dec~~;~~180~~(3):~~519-30~~. doi: 10.~~1016~~/~~j.jsb.2012.09.006. Epub 2012 , Sep 19~~. PMID:~~23000701~~<ref>PMID:~~23000701~~</ref>	+	Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog.,Biou V, Adaixo RJD, Chami M, Coureux PD, Laurent B, Enguene VYN, de Amorim GC, Izadi-Pruneyre N, Malosse C, Chamot-Rooke J, Stahlberg H, Delepelaire P Commun Biol. 2022 Apr 13;5(1):355. doi: 10.1038/s42003-022-03306-y. PMID:35418619<ref>PMID:35418619</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 12:46, 13 October 2021

OCA — Wed, 13 Oct 2021 12:46:02 GMT

←Older revision		Revision as of 12:46, 13 October 2021
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	==Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy==		==Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy==
-	<StructureSection load='6ye4' size='340' side='right'caption='[[6ye4]]' scene=''>	+	<StructureSection load='6ye4' size='340' side='right'caption='[[6ye4]], [[Resolution\|resolution]] 3.20Å' 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=6YE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ye4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE4 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=6ye4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye4 OCA], [https://pdbe.org/6ye4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye4 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=PGT:(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+STEARATE'>PGT</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">exbB, FG174_21755, PWN146_03792 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889])</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=6ye4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye4 OCA], [https://pdbe.org/6ye4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye4 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.
		+
		+	RELION: implementation of a Bayesian approach to cryo-EM structure determination.,Scheres SH J Struct Biol. 2012 Dec;180(3):519-30. doi: 10.1016/j.jsb.2012.09.006. Epub 2012 , Sep 19. PMID:23000701<ref>PMID:23000701</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ye4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ExbB\|ExbB]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Biou V]]	+	[[Category: Biou, V]]
-	[[Category: Chami M]]	+	[[Category: Chami, M]]
-	[[Category: Coureux PD]]	+	[[Category: Coureux, P D]]
-	[[Category: Delepelaire P]]	+	[[Category: Delepelaire, P]]
		+	[[Category: Iron uptake]]
		+	[[Category: Membrane protein]]
		+	[[Category: Metal transport]]
		+	[[Category: Proton transfer]]
		+	[[Category: Tonb complex]]

OCA at 10:29, 31 March 2021

OCA — Wed, 31 Mar 2021 10:29:57 GMT

←Older revision		Revision as of 10:29, 31 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6ye4 ~~is ON HOLD until Paper Publication~~	+	==Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy==
-		+	<StructureSection load='6ye4' size='340' side='right'caption='[[6ye4]]' scene=''>
-	~~Authors~~: ~~Biou~~, V., ~~Delepelaire, P~~., ~~Coureux, P~~.D., ~~Chami~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE4 FirstGlance]. <br>
-	~~Description: Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy~~	+	</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=6ye4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye4 OCA], [https://pdbe.org/6ye4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye4 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Chami, M~~]]	+	__TOC__
-	[[Category: ~~Coureux, P.D~~]]	+	</StructureSection>
-	[[Category: ~~Biou, V~~]]	+	[[Category: Large Structures]]
-	[[Category: Delepelaire, P]]	+	[[Category: Biou V]]
		+	[[Category: Chami M]]
		+	[[Category: Coureux PD]]
		+	[[Category: Delepelaire P]]

OCA at 04:21, 22 April 2020

OCA — Wed, 22 Apr 2020 04:21:49 GMT

←Older revision		Revision as of 04:21, 22 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ye4 is ON HOLD	+	The entry 6ye4 is ON HOLD until Paper Publication

	Authors: Biou, V., Delepelaire, P., Coureux, P.D., Chami, M.		Authors: Biou, V., Delepelaire, P., Coureux, P.D., Chami, M.
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	Description: Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy		Description: Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Biou, V]]
-	[[Category: Delepelaire, P]]
	[[Category: Chami, M]]		[[Category: Chami, M]]
	[[Category: Coureux, P.D]]		[[Category: Coureux, P.D]]
		+	[[Category: Biou, V]]
		+	[[Category: Delepelaire, P]]

OCA: Protected "6ye4" [edit=sysop:move=sysop]

OCA — Wed, 01 Apr 2020 07:43:10 GMT

Protected "6ye4" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:43, 1 April 2020

OCA: New page: '''Unreleased structure''' The entry 6ye4 is ON HOLD Authors: Biou, V., Delepelaire, P., Coureux, P.D., Chami, M. Description: Structure of ExbB pentamer from Serratia marcescens by si...

OCA — Wed, 01 Apr 2020 07:43:09 GMT

New page: '''Unreleased structure''' The entry 6ye4 is ON HOLD Authors: Biou, V., Delepelaire, P., Coureux, P.D., Chami, M. Description: Structure of ExbB pentamer from Serratia marcescens by si...

New page

'''Unreleased structure'''

The entry 6ye4 is ON HOLD

Authors: Biou, V., Delepelaire, P., Coureux, P.D., Chami, M.

Description: Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy
[[Category: Unreleased Structures]]
[[Category: Biou, V]]
[[Category: Delepelaire, P]]
[[Category: Chami, M]]
[[Category: Coureux, P.D]]