4o5j - Revision history

OCA at 08:56, 18 January 2023

OCA — Wed, 18 Jan 2023 08:56:43 GMT

←Older revision		Revision as of 08:56, 18 January 2023
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	==Crystal structure of SabA from Helicobacter pylori==		==Crystal structure of SabA from Helicobacter pylori==
-	<StructureSection load='4o5j' size='340' side='right' caption='[[4o5j]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4o5j' size='340' side='right'caption='[[4o5j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o5j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4O5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o5j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O5J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">C694_03730, SabA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=4o5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5j OCA], [https://pdbe.org/4o5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o5j RCSB], [https://www.ebi.ac.uk/pdbsum/4o5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5j 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=4o5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5j OCA], [~~http~~://pdbe.org/4o5j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4o5j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4o5j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5j ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2I8VBX7_HELPX A0A2I8VBX7_HELPX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori]]	+	[[Category: Helicobacter pylori 26695]]
-	[[Category: ~~Nguyen, S T.S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Pang, S S~~]]	+	[[Category: Nguyen STS]]
-	[[Category: ~~Whisstock, J C~~]]	+	[[Category: Pang SS]]
-	[[Category: ~~Adhesin]]~~	+	[[Category: Whisstock JC]]
-	~~[[Category: Carbohydrate/sugar binding]]~~	+
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Helicobacter pylori]]~~	+
-	~~[[Category: Outer membrane protein]]~~	+
-	~~[[Category: Tetratricopeptide repeat~~]]	+

OCA at 10:16, 11 August 2016

OCA — Thu, 11 Aug 2016 10:16:53 GMT

←Older revision		Revision as of 10:16, 11 August 2016
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		+
	==Crystal structure of SabA from Helicobacter pylori==		==Crystal structure of SabA from Helicobacter pylori==
	<StructureSection load='4o5j' size='340' side='right' caption='[[4o5j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4o5j' size='340' side='right' caption='[[4o5j]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">C694_03730, SabA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">C694_03730, SabA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=4o5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o5j RCSB], [http://www.ebi.ac.uk/pdbsum/4o5j PDBsum]</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=4o5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5j OCA], [http://pdbe.org/4o5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o5j RCSB], [http://www.ebi.ac.uk/pdbsum/4o5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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>
	</div>		</div>
		+	<div class="pdbe-citations 4o5j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:32, 5 January 2015

OCA — Mon, 05 Jan 2015 09:32:14 GMT

←Older revision		Revision as of 09:32, 5 January 2015
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-	~~{{STRUCTURE_4o5j\| PDB~~=4o5j \| ~~SCENE~~= }}	+	==Crystal structure of SabA from Helicobacter pylori==
-	===~~Crystal~~ structure ~~of SabA~~ from ~~Helicobacter~~ pylori===	+	<StructureSection load='4o5j' size='340' side='right' caption='[[4o5j]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24375407}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4o5j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">C694_03730, SabA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=4o5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o5j RCSB], [http://www.ebi.ac.uk/pdbsum/4o5j PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The gastric pathogen Helicobacter pylori is a major cause of acute chronic gastritis and the development of stomach and duodenal ulcers. Chronic infection furthermore pre-disposes to the development of gastric cancer. Crucial to H. pylori survival within the hostile environment of the digestive system are the adhesins SabA and BabA; these molecules belong to the same protein family and permit the bacteria to bind tightly to sugar moieties LewisB and sialyl-LewisX, respectively, on the surface of epithelial cells lining the stomach and duodenum. Currently, no representative SabA / BabA structure has been determined, however, hampering the development of strategies to eliminate persistent H. pylori infections that fail to respond to conventional therapy. Here, using X-ray crystallography, we show that the soluble extracellular adhesin domain of SabA shares distant similarity to the tetratricopeptide repeat (TPR) fold family. The molecule broadly resembles a golf putter in shape, with the head region featuring a large cavity surrounded by loops that vary in sequence between different H. pylori strains. The N-terminal and C-terminal helices protrude at right angles from the head domain and together form a shaft that connects to a predicted outer membrane protein (OMP)-like beta-barrel trans-membrane domain. Using surface plasmon resonance, we were able to detect binding of the SabA adhesin domain to sialyl-LewisX and LewisX but not to LewisA, LewisB or LewisY. Substitution of the highly conserved glutamine residue 159 in the predicted ligand-binding pocket abrogates the binding of the SabA adhesin domain to sialyl-LewisX and LewisX. Taken together, these data suggest that the adhesin domain of SabA is sufficient in isolation for specific ligand binding.

-	~~==About this Structure==~~	+	The three-dimensional structure of the extracellular adhesion domain of the sialic acid-binding adhesin SabA from Helicobacter pylori.,Pang SS, Nguyen ST, Perry AJ, Day CJ, Panjikar S, Tiralongo J, Whisstock JC, Kwok T J Biol Chem. 2013 Dec 27. PMID:24375407<ref>PMID:24375407</ref>
-	~~[[4o5j]] is a 1 chain~~ structure~~. Full crystallographic information is available~~ from ~~[http://oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4O5J OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024375407</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Nguyen, S T.S.]]	+	== References ==
-	[[Category: Pang, S S.]]	+	<references/>
-	[[Category: Whisstock, J C.]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Campylobacter pylori]]
		+	[[Category: Nguyen, S T.S]]
		+	[[Category: Pang, S S]]
		+	[[Category: Whisstock, J C]]
	[[Category: Adhesin]]		[[Category: Adhesin]]
	[[Category: Carbohydrate/sugar binding]]		[[Category: Carbohydrate/sugar binding]]

OCA at 08:10, 26 March 2014

OCA — Wed, 26 Mar 2014 08:10:15 GMT

←Older revision		Revision as of 08:10, 26 March 2014
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	{{STRUCTURE_4o5j\| PDB=4o5j \| SCENE= }}		{{STRUCTURE_4o5j\| PDB=4o5j \| SCENE= }}
	===Crystal structure of SabA from Helicobacter pylori===		===Crystal structure of SabA from Helicobacter pylori===
		+	{{ABSTRACT_PUBMED_24375407}}

	==About this Structure==		==About this Structure==
	[[4o5j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5J OCA].		[[4o5j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5J OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024375407</ref><references group="xtra"/><references/>
	[[Category: Nguyen, S T.S.]]		[[Category: Nguyen, S T.S.]]
	[[Category: Pang, S S.]]		[[Category: Pang, S S.]]

OCA at 12:17, 1 January 2014

OCA — Wed, 01 Jan 2014 12:17:48 GMT

←Older revision		Revision as of 12:17, 1 January 2014
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4o5j\| PDB=4o5j \| SCENE= }}
		+	===Crystal structure of SabA from Helicobacter pylori===

-	~~The entry~~ 4o5j is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4o5j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5J OCA].
-	~~Authors~~: ~~Pang, S~~.S., Nguyen, S.T.S., Whisstock, J.C.	+	[[Category: Nguyen, S T.S.]]
-		+	[[Category: Pang, S S.]]
-	~~Description~~: ~~Crystal structure of SabA from~~ Helicobacter pylori	+	[[Category: Whisstock, J C.]]
		+	[[Category: Adhesin]]
		+	[[Category: Carbohydrate/sugar binding]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Helicobacter pylori]]
		+	[[Category: Outer membrane protein]]
		+	[[Category: Tetratricopeptide repeat]]

OCA: Protected "4o5j" [edit=sysop:move=sysop]

OCA — Wed, 25 Dec 2013 09:34:59 GMT

Protected "4o5j" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:34, 25 December 2013

OCA: New page: '''Unreleased structure''' The entry 4o5j is ON HOLD Authors: Pang, S.S., Nguyen, S.T.S., Whisstock, J.C. Description: Crystal structure of SabA from Helicobacter pylori

OCA — Wed, 25 Dec 2013 09:34:58 GMT

New page: '''Unreleased structure''' The entry 4o5j is ON HOLD Authors: Pang, S.S., Nguyen, S.T.S., Whisstock, J.C. Description: Crystal structure of SabA from Helicobacter pylori

New page

'''Unreleased structure'''

The entry 4o5j is ON HOLD

Authors: Pang, S.S., Nguyen, S.T.S., Whisstock, J.C.

Description: Crystal structure of SabA from Helicobacter pylori