6dwi - Revision history

OCA at 06:14, 11 October 2023

OCA — Wed, 11 Oct 2023 06:14:55 GMT

←Older revision		Revision as of 06:14, 11 October 2023
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	<StructureSection load='6dwi' size='340' side='right'caption='[[6dwi]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='6dwi' size='340' side='right'caption='[[6dwi]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dwi]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6DWI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dwi]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DWI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HD4:4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol'>HD4</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]] 2.39Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dw2\|6dw2]], [[6dwa\|6dwa]], [[6dwc\|6dwc]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HD4:4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol'>HD4</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=6dwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwi OCA], [~~http~~://pdbe.org/6dwi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dwi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dwi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwi 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=6dwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwi OCA], [https://pdbe.org/6dwi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dwi RCSB], [https://www.ebi.ac.uk/pdbsum/6dwi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fong, R]]	+	[[Category: Fong R]]
-	[[Category: Lupardus~~, P J]]~~	+	[[Category: Lupardus PJ]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Staphylococcus aureus]]~~	+
-	~~[[Category: Wall teichoic acid]]~~	+
-	~~[[Category: Wta~~]]	+

OCA at 09:08, 11 November 2020

OCA — Wed, 11 Nov 2020 09:08:33 GMT

←Older revision		Revision as of 09:08, 11 November 2020
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	==Structure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog==		==Structure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog==
-	<StructureSection load='6dwi' size='340' side='right' caption='[[6dwi]], [[Resolution\|resolution]] 2.39Å' scene=''>	+	<StructureSection load='6dwi' size='340' side='right'caption='[[6dwi]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dwi]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DWI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dwi]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DWI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HD4:4-O-[2-~~(acetylamino)~~-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol'>HD4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HD4:4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol'>HD4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dw2\|6dw2]], [[6dwa\|6dwa]], [[6dwc\|6dwc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dw2\|6dw2]], [[6dwa\|6dwa]], [[6dwc\|6dwc]]</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=6dwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwi OCA], [http://pdbe.org/6dwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dwi RCSB], [http://www.ebi.ac.uk/pdbsum/6dwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwi 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=6dwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwi OCA], [http://pdbe.org/6dwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dwi RCSB], [http://www.ebi.ac.uk/pdbsum/6dwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Fong, R]]		[[Category: Fong, R]]
	[[Category: Lupardus, P J]]		[[Category: Lupardus, P J]]

OCA at 10:30, 5 September 2018

OCA — Wed, 05 Sep 2018 10:30:26 GMT

←Older revision		Revision as of 10:30, 5 September 2018
Line 3:		Line 3:
	<StructureSection load='6dwi' size='340' side='right' caption='[[6dwi]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='6dwi' size='340' side='right' caption='[[6dwi]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dwi]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DWI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dwi]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DWI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HD4:4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol'>HD4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HD4:4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol'>HD4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dw2\|6dw2]], [[6dwa\|6dwa]], [[6dwc\|6dwc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dw2\|6dw2]], [[6dwa\|6dwa]], [[6dwc\|6dwc]]</td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Fong, R]]		[[Category: Fong, R]]
	[[Category: Lupardus, P J]]		[[Category: Lupardus, P J]]

OCA at 07:29, 29 August 2018

OCA — Wed, 29 Aug 2018 07:29:20 GMT

←Older revision		Revision as of 07:29, 29 August 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6dwi is ~~ON HOLD until Paper~~ Publication	+	==Structure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog==
		+	<StructureSection load='6dwi' size='340' side='right' caption='[[6dwi]], [[Resolution\|resolution]] 2.39Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dwi]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DWI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HD4:4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol'>HD4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dw2\|6dw2]], [[6dwa\|6dwa]], [[6dwc\|6dwc]]</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=6dwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwi OCA], [http://pdbe.org/6dwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dwi RCSB], [http://www.ebi.ac.uk/pdbsum/6dwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a growing health threat worldwide. Efforts to identify novel antibodies that target S. aureus cell surface antigens are a promising direction in the development of antibiotics that can halt MRSA infection. We biochemically and structurally characterized three patient-derived MRSA-targeting antibodies that bind to wall teichoic acid (WTA), which is a polyanionic surface glycopolymer. In S. aureus, WTA exists in both alpha- and beta-forms, based on the stereochemistry of attachment of a N-acetylglucosamine residue to the repeating phosphoribitol sugar unit. We identified a panel of antibodies cloned from human patients that specifically recognize the alpha or beta form of WTA, and can bind with high affinity to pathogenic wild-type strains of S. aureus bacteria. To investigate how the beta-WTA specific antibodies interact with their target epitope, we determined the X-ray crystal structures of the three beta-WTA specific antibodies, 4462, 4497, and 6078 (Protein Data Bank IDs 6DWI, 6DWA, and 6DW2, respectively), bound to a synthetic WTA epitope. These structures reveal that all three of these antibodies, while utilizing distinct antibody complementarity-determining region sequences and conformations to interact with beta-WTA, fulfill two recognition principles: binding to the beta-GlcNAc pyranose core and triangulation of WTA phosphate residues with polar contacts. These studies reveal the molecular basis for targeting a unique S. aureus cell surface epitope and highlight the power of human patient-based antibody discovery techniques for finding novel pathogen-targeting therapeutics.

-	~~Authors: Fong~~, R., ~~Lupardus~~, P.J.	+	Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid.,Fong R, Kajihara K, Chen M, Hotzel I, Mariathasan S, Hazenbos WLW, Lupardus PJ MAbs. 2018 Aug 13:1-13. doi: 10.1080/19420862.2018.1501252. PMID:30102105<ref>PMID:30102105</ref>

-	~~Description: Structure~~ of the ~~4462 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Lupardus, P.J]]~~	+	<div class="pdbe-citations 6dwi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fong, R]]		[[Category: Fong, R]]
		+	[[Category: Lupardus, P J]]
		+	[[Category: Antibody]]
		+	[[Category: Fab]]
		+	[[Category: Immune system]]
		+	[[Category: Staphylococcus aureus]]
		+	[[Category: Wall teichoic acid]]
		+	[[Category: Wta]]

OCA at 05:26, 18 July 2018

OCA — Wed, 18 Jul 2018 05:26:22 GMT

←Older revision		Revision as of 05:26, 18 July 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Fong, R., Lupardus, P.J.		Authors: Fong, R., Lupardus, P.J.

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

OCA — Wed, 04 Jul 2018 05:47:53 GMT

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

←Older revision

Revision as of 05:47, 4 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dwi is ON HOLD Authors: Fong, R., Lupardus, P.J. Description: Structure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall te...

OCA — Wed, 04 Jul 2018 05:47:52 GMT

New page: '''Unreleased structure''' The entry 6dwi is ON HOLD Authors: Fong, R., Lupardus, P.J. Description: Structure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall te...

New page

'''Unreleased structure'''

The entry 6dwi is ON HOLD

Authors: Fong, R., Lupardus, P.J.

Description: Structure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog
[[Category: Unreleased Structures]]
[[Category: Lupardus, P.J]]
[[Category: Fong, R]]