5mdq - Revision history

OCA at 18:40, 1 November 2023

OCA — Wed, 01 Nov 2023 18:40:06 GMT

←Older revision		Revision as of 18:40, 1 November 2023
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	==Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi==		==Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi==
-	<StructureSection load='5mdq' size='340' side='right' caption='[[5mdq]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5mdq' size='340' side='right'caption='[[5mdq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdq]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_harveyi"_johnson_and_shunk_1936 "achromobacter~~ harveyi~~" johnson and shunk 1936~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MDQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_harveyi Vibrio harveyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MDQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=NA:SODIUM+ION'>NA</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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>chiP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~669~~ "~~Achromobacter harveyi~~" ~~Johnson and Shunk 1936])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=5mdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdq OCA], [~~http~~://pdbe.org/5mdq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mdq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mdq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdq 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=5mdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdq OCA], [https://pdbe.org/5mdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mdq RCSB], [https://www.ebi.ac.uk/pdbsum/5mdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/L0RVU0_VIBHA L0RVU0_VIBHA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5mdq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mdq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Porin 3D structures\|Porin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Achromobacter harveyi johnson and shunk 1936~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Berg, B van den~~]]	+	[[Category: Vibrio harveyi]]
-	[[Category: Zahn, M]]	+	[[Category: Zahn M]]
-	[[Category: ~~Outer membrane protein vibrio harveyi porin channel]]~~	+	[[Category: Van den Berg B]]
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 20:40, 24 January 2018

OCA — Wed, 24 Jan 2018 20:40:13 GMT

←Older revision		Revision as of 20:40, 24 January 2018
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	<StructureSection load='5mdq' size='340' side='right' caption='[[5mdq]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5mdq' size='340' side='right' caption='[[5mdq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdq]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_harveyi"_johnson_and_shunk_1936 "achromobacter harveyi" johnson and shunk 1936]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">chiP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=669 "Achromobacter harveyi" Johnson and Shunk 1936])</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=5mdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdq OCA], [http://pdbe.org/5mdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdq RCSB], [http://www.ebi.ac.uk/pdbsum/5mdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdq 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=5mdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdq OCA], [http://pdbe.org/5mdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdq RCSB], [http://www.ebi.ac.uk/pdbsum/5mdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chitin, an insoluble polymer of N-acetylglucosamine, is one of the most abundant biopolymers on Earth. By degrading chitin, chitinolytic bacteria such as Vibrio harveyi are critical for chitin recycling and maintenance of carbon and nitrogen cycles in the world's oceans. A decisive step in chitin degradation is the uptake of chito-oligosaccharides by an outer membrane protein channel named chitoporin (ChiP). Here, we report X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides. Structures without bound sugar reveal a trimeric assembly with an unprecedented closing of the transport pore by the N-terminus of a neighboring subunit. Substrate binding ejects the pore plug to open the transport channel. Together with molecular dynamics simulations, electrophysiology and in vitro transport assays our data provide an explanation for the exceptional affinity of ChiP for chito-oligosaccharides and point to an important role of the N-terminal gate in substrate transport.
		+
		+	Structural basis for chitin acquisition by marine Vibrio species.,Aunkham A, Zahn M, Kesireddy A, Pothula KR, Schulte A, Basle A, Kleinekathofer U, Suginta W, van den Berg B Nat Commun. 2018 Jan 15;9(1):220. doi: 10.1038/s41467-017-02523-y. PMID:29335469<ref>PMID:29335469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5mdq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Achromobacter harveyi johnson and shunk 1936]]
	[[Category: Berg, B van den]]		[[Category: Berg, B van den]]
	[[Category: Zahn, M]]		[[Category: Zahn, M]]
	[[Category: Outer membrane protein vibrio harveyi porin channel]]		[[Category: Outer membrane protein vibrio harveyi porin channel]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 06:07, 20 December 2017

OCA — Wed, 20 Dec 2017 06:07:21 GMT

←Older revision		Revision as of 06:07, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5mdq is ON HOLD until Paper Publication~~	+	==Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi==
-		+	<StructureSection load='5mdq' size='340' side='right' caption='[[5mdq]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors: Zahn, M., van den Berg, B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5mdq]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDQ FirstGlance]. <br>
-	~~Description:~~ Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5mdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdq OCA], [http://pdbe.org/5mdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdq RCSB], [http://www.ebi.ac.uk/pdbsum/5mdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdq ProSAT]</span></td></tr>
-	[[Category: ~~Van Den~~ Berg, B]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Berg, B van den]]
	[[Category: Zahn, M]]		[[Category: Zahn, M]]
		+	[[Category: Outer membrane protein vibrio harveyi porin channel]]
		+	[[Category: Sugar binding protein]]

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

OCA — Fri, 09 Dec 2016 16:41:21 GMT

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

←Older revision

Revision as of 16:41, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mdq is ON HOLD until Paper Publication Authors: Zahn, M., van den Berg, B. Description: Crystal structure of outer membrane expressed Chitoporin V...

OCA — Fri, 09 Dec 2016 16:41:20 GMT

New page: '''Unreleased structure''' The entry 5mdq is ON HOLD until Paper Publication Authors: Zahn, M., van den Berg, B. Description: Crystal structure of outer membrane expressed Chitoporin V...

New page

'''Unreleased structure'''

The entry 5mdq is ON HOLD until Paper Publication

Authors: Zahn, M., van den Berg, B.

Description: Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi
[[Category: Unreleased Structures]]
[[Category: Van Den Berg, B]]
[[Category: Zahn, M]]