5fvn - Revision history

OCA at 07:47, 7 February 2024

OCA — Wed, 07 Feb 2024 07:47:47 GMT

←Older revision		Revision as of 07:47, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FVN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FVN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</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]] 1.45Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</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=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [https://pdbe.org/5fvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [https://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn 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=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [https://pdbe.org/5fvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [https://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q93K99_ENTCL Q93K99_ENTCL]		[https://www.uniprot.org/uniprot/Q93K99_ENTCL Q93K99_ENTCL]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin-LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin-LPS interactions and a bridging calcium ion.
-
-	Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis.,Arunmanee W, Pathania M, Solovyova AS, Le Brun AP, Ridley H, Basle A, van den Berg B, Lakey JH Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):E5034-43. doi:, 10.1073/pnas.1602382113. Epub 2016 Aug 4. PMID:27493217<ref>PMID:27493217</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5fvn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Porin 3D structures\|Porin 3D structures]]		*[[Porin 3D structures\|Porin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:39, 8 March 2023

OCA — Wed, 08 Mar 2023 07:39:37 GMT

←Older revision		Revision as of 07:39, 8 March 2023
Line 1:		Line 1:

-	==X-ray crystal structure of Enterobacter cloacae OmpE36 porin==	+	==X-ray crystal structure of Enterobacter cloacae OmpE36 porin.==
	<StructureSection load='5fvn' size='340' side='right'caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='5fvn' size='340' side='right'caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter~~ cloacae~~" (jordan 1890) bergey et al. 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FVN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FVN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=~~KDO~~:3-~~DEOXY~~-D-MANNO-~~OCT-2-ULOSONIC+ACID~~'>~~KDO~~</scene>, <scene name='pdbligand=~~MYR~~:~~MYRISTIC~~+~~ACID~~'>~~MYR~~</scene>, <scene name='pdbligand=~~PO4~~:~~PHOSPHATE~~+~~ION~~'>~~PO4~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE~~+~~ION~~'>~~SO4~~</scene>, <scene name='pdbligand=~~GMH~~:~~L-GLYCERO-D-MANNO-HEPTOPYRANOSE~~'>~~GMH~~</scene>, <scene name='pdbligand=~~GP1~~:~~GLUCOSAMINE~~+~~1-PHOSPHATE~~'>~~GP1~~</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</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=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [https://pdbe.org/5fvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [https://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn 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=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [https://pdbe.org/5fvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [https://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q93K99_ENTCL Q93K99_ENTCL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterobacter cloacae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arunmanee, W]]	+	[[Category: Arunmanee W]]
-	[[Category: Basle, A]]	+	[[Category: Basle A]]
-	~~[[Category: Berg, B van den~~]]	+	[[Category: Brun A]]
-	[[Category: Brun, A]]	+	[[Category: Lakey JH]]
-	[[Category: Lakey~~, J H~~]]	+	[[Category: Pathania M]]
-	[[Category: Pathania, M]]	+	[[Category: Ridley H]]
-	[[Category: Ridley, H]]	+	[[Category: Soloyova A]]
-	[[Category: Soloyova, A]]	+	[[Category: Van den Berg B]]
-	[[Category: ~~Channel]]~~	+
-	~~[[Category: Lp]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Outer membrane protein]]~~	+
-	~~[[Category: Porin]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 02:59, 21 April 2022

OCA — Thu, 21 Apr 2022 02:59:49 GMT

←Older revision		Revision as of 02:59, 21 April 2022
Line 3:		Line 3:
	<StructureSection load='5fvn' size='340' side='right'caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='5fvn' size='340' side='right'caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FVN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FVN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT~~</scene>, <scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1~~</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [~~http~~://pdbe.org/5fvn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn 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=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [https://pdbe.org/5fvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [https://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:17, 29 July 2020

OCA — Wed, 29 Jul 2020 11:17:07 GMT

←Older revision		Revision as of 11:17, 29 July 2020
Line 1:		Line 1:

	==X-ray crystal structure of Enterobacter cloacae OmpE36 porin==		==X-ray crystal structure of Enterobacter cloacae OmpE36 porin==
-	<StructureSection load='5fvn' size='340' side='right' caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='5fvn' size='340' side='right'caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FVN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FVN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=~~GMH~~:L-~~GLYCERO-D-MANNO-HEPTOPYRANOSE~~'>~~GMH~~</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=~~L1L~~:~~[(2R,3R,4R,5S,6R)-3-AZANYL-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-2-YL]~~+~~DIHYDROGEN+PHOSPHATE~~'>~~L1L~~</scene>, <scene name='pdbligand=~~MYR~~:~~MYRISTIC~~+~~ACID~~'>~~MYR~~</scene>, <scene name='pdbligand=~~PO4~~:~~PHOSPHATE~~+ION'>~~PO4~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=GP1:GLUCOSAMINE+1-PHOSPHATE'>GP1</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [http://pdbe.org/5fvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [http://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [http://pdbe.org/5fvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [http://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:

	==See Also==		==See Also==
-	*[[Porin\|Porin]]	+	*[[Porin 3D structures\|Porin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arunmanee, W]]		[[Category: Arunmanee, W]]
	[[Category: Basle, A]]		[[Category: Basle, A]]

OCA at 09:18, 30 January 2019

OCA — Wed, 30 Jan 2019 09:18:16 GMT

←Older revision		Revision as of 09:18, 30 January 2019
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5fvn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fvn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Porin\|Porin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:41, 22 February 2018

OCA — Thu, 22 Feb 2018 07:41:02 GMT

←Older revision		Revision as of 07:41, 22 February 2018
Line 3:		Line 3:
	<StructureSection load='5fvn' size='340' side='right' caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='5fvn' size='340' side='right' caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FVN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FVN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=~~MYR~~:~~MYRISTIC~~+~~ACID~~'>~~MYR~~</scene>, <scene name='pdbligand=~~PO4~~:~~PHOSPHATE~~+~~ION~~'>~~PO4~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE~~+ION'>~~SO4~~</scene>, <scene name='pdbligand=~~GMH~~:~~L-GLYCERO-D-MANNO-HEPTOPYRANOSE~~'>~~GMH~~</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M~~</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=L1L:[(2R,3R,4R,5S,6R)-3-AZANYL-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-2-YL]+DIHYDROGEN+PHOSPHATE'>L1L</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=L1L:[(2R,3R,4R,5S,6R)-3-AZANYL-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-2-YL]+DIHYDROGEN+PHOSPHATE'>L1L</scene></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [http://pdbe.org/5fvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [http://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [http://pdbe.org/5fvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [http://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 22:
	[[Category: Arunmanee, W]]		[[Category: Arunmanee, W]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
		+	[[Category: Berg, B van den]]
	[[Category: Brun, A]]		[[Category: Brun, A]]
	[[Category: Lakey, J H]]		[[Category: Lakey, J H]]
Line 28:		Line 28:
	[[Category: Ridley, H]]		[[Category: Ridley, H]]
	[[Category: Soloyova, A]]		[[Category: Soloyova, A]]
-	[[Category: VandenBerg, B]]
	[[Category: Channel]]		[[Category: Channel]]
	[[Category: Lp]]		[[Category: Lp]]

OCA at 05:22, 9 September 2016

OCA — Fri, 09 Sep 2016 05:22:54 GMT

←Older revision		Revision as of 05:22, 9 September 2016
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [http://pdbe.org/5fvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [http://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [http://pdbe.org/5fvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [http://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin-LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin-LPS interactions and a bridging calcium ion.
		+
		+	Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis.,Arunmanee W, Pathania M, Solovyova AS, Le Brun AP, Ridley H, Basle A, van den Berg B, Lakey JH Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):E5034-43. doi:, 10.1073/pnas.1602382113. Epub 2016 Aug 4. PMID:27493217<ref>PMID:27493217</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fvn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:24, 10 August 2016

OCA — Wed, 10 Aug 2016 16:24:17 GMT

←Older revision		Revision as of 16:24, 10 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fvn ~~is ON HOLD~~	+	==X-ray crystal structure of Enterobacter cloacae OmpE36 porin==
-		+	<StructureSection load='5fvn' size='340' side='right' caption='[[5fvn]], [[Resolution\|resolution]] 1.45Å' scene=''>
-	~~Authors~~: ~~Arunmanee, W~~., ~~Pathania~~, M., ~~Soloyova~~, A., ~~Brun~~, A., ~~Ridley~~, H., ~~Basle~~, A., ~~vandenBerg~~, B., ~~Lakey~~, J.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fvn]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FVN FirstGlance]. <br>
-	~~Description~~: ~~X-ray crystal structure of Enterobacter cloacae OmpE36 porin~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=Z9M:2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>Z9M</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=L1L:[(2R,3R,4R,5S,6R)-3-AZANYL-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-2-YL]+DIHYDROGEN+PHOSPHATE'>L1L</scene></td></tr>
-	[[Category: ~~Vandenberg~~, B]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5fvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvn OCA], [http://pdbe.org/5fvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvn RCSB], [http://www.ebi.ac.uk/pdbsum/5fvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvn ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arunmanee, W]]
		+	[[Category: Basle, A]]
		+	[[Category: Brun, A]]
		+	[[Category: Lakey, J H]]
	[[Category: Pathania, M]]		[[Category: Pathania, M]]
-	[[Category: ~~Arunmanee~~, W]]	+	[[Category: Ridley, H]]
	[[Category: Soloyova, A]]		[[Category: Soloyova, A]]
-	[[Category: ~~Ridley~~, H]]	+	[[Category: VandenBerg, B]]
-	[[Category: ~~Brun, A~~]]	+	[[Category: Channel]]
-	[[Category: ~~Lakey, J.H~~]]	+	[[Category: Lp]]
-	[[Category: ~~Basle, A~~]]	+	[[Category: Membrane protein]]
		+	[[Category: Outer membrane protein]]
		+	[[Category: Porin]]
		+	[[Category: Trimer]]

OCA at 10:52, 20 June 2016

OCA — Mon, 20 Jun 2016 10:52:44 GMT

←Older revision		Revision as of 10:52, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fvn is ON HOLD ~~until sometime in the future~~	+	The entry 5fvn is ON HOLD

	Authors: Arunmanee, W., Pathania, M., Soloyova, A., Brun, A., Ridley, H., Basle, A., vandenBerg, B., Lakey, J.H.		Authors: Arunmanee, W., Pathania, M., Soloyova, A., Brun, A., Ridley, H., Basle, A., vandenBerg, B., Lakey, J.H.

OCA: Protected "5fvn" [edit=sysop:move=sysop]

OCA — Sun, 21 Feb 2016 00:27:50 GMT

Protected "5fvn" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:27, 21 February 2016