4ods - Revision history

OCA at 17:10, 20 September 2023

OCA — Wed, 20 Sep 2023 17:10:56 GMT

←Older revision		Revision as of 17:10, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ODS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ODS 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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [https://pdbe.org/4ods PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [https://www.ebi.ac.uk/pdbsum/4ods PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ods ProSAT]</span></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]] 1.94Å</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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [https://pdbe.org/4ods PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [https://www.ebi.ac.uk/pdbsum/4ods PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ods ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:19, 25 January 2023

OCA — Wed, 25 Jan 2023 07:19:12 GMT

←Older revision		Revision as of 07:19, 25 January 2023
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	<StructureSection load='4ods' size='340' side='right'caption='[[4ods]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='4ods' size='340' side='right'caption='[[4ods]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ODS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ODS FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4odv\|4odv]], [[4odw\|4odw]], [[4ody\|4ody]], [[4odz\|4odz]], [[4oe0\|4oe0]]</td></tr>	+	</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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [https://pdbe.org/4ods PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [https://www.ebi.ac.uk/pdbsum/4ods PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ods 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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [~~http~~://pdbe.org/4ods PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ods PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ods ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Evans~~, S V~~]]	+	[[Category: Evans SV]]
-	[[Category: Haji-Ghassemi, O]]	+	[[Category: Haji-Ghassemi O]]
-	~~[[Category: Carbohydrate binding]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 05:31, 13 February 2020

OCA — Thu, 13 Feb 2020 05:31:51 GMT

←Older revision		Revision as of 05:31, 13 February 2020
Line 1:		Line 1:

	==Unliganded Fab structure of lipid A-specific antibody S55-3==		==Unliganded Fab structure of lipid A-specific antibody S55-3==
-	<StructureSection load='4ods' size='340' side='right' caption='[[4ods]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='4ods' size='340' side='right'caption='[[4ods]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ODS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ODS FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Evans, S V]]		[[Category: Evans, S V]]

OCA at 08:24, 22 November 2017

OCA — Wed, 22 Nov 2017 08:24:38 GMT

←Older revision		Revision as of 08:24, 22 November 2017
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		+
	==Unliganded Fab structure of lipid A-specific antibody S55-3==		==Unliganded Fab structure of lipid A-specific antibody S55-3==
	<StructureSection load='4ods' size='340' side='right' caption='[[4ods]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='4ods' size='340' side='right' caption='[[4ods]], [[Resolution\|resolution]] 1.94Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ODS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ODS FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4odv\|4odv]], [[4odw\|4odw]], [[4ody\|4ody]], [[4odz\|4odz]], [[4oe0\|4oe0]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4odv\|4odv]], [[4odw\|4odw]], [[4ody\|4ody]], [[4odz\|4odz]], [[4oe0\|4oe0]]</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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [http://pdbe.org/4ods PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [http://www.ebi.ac.uk/pdbsum/4ods 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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [http://pdbe.org/4ods PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [http://www.ebi.ac.uk/pdbsum/4ods PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ods ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:39, 7 October 2015

OCA — Wed, 07 Oct 2015 07:39:01 GMT

←Older revision		Revision as of 07:39, 7 October 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ODS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ODS FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4odv\|4odv]], [[4odw\|4odw]], [[4ody\|4ody]], [[4odz\|4odz]], [[4oe0\|4oe0]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4odv\|4odv]], [[4odw\|4odw]], [[4ody\|4ody]], [[4odz\|4odz]], [[4oe0\|4oe0]]</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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [http://www.ebi.ac.uk/pdbsum/4ods 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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [http://pdbe.org/4ods PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [http://www.ebi.ac.uk/pdbsum/4ods PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Septic shock is a leading cause of death, and, results from an inflammatory cascade triggered by the presence of microbial products in the blood. Certain LPS from Gram-negative bacteria are very potent inducers and responsible for a high percentage of septic shock cases. Despite decades of research, mAbs specific for lipid A (the endotoxic principle of LPS) have not been successfully developed into a clinical treatment for sepsis. To understand the molecular basis for the observed inability to translate in vitro specificity for lipid A into clinical potential, the structures of antigen binding fragments of mAbs S1-15 and A6 have been determined unliganded and in complex with lipid A carbohydrate backbone. The two antibodies have separate germ-line origins that generate two markedly different combining-site pockets that are complementary both in shape and charge to the antigen. MAb A6 binds lipid A through both variable light and heavy chain residues, while S1-15 utilizes exclusively the variable heavy chain. Both antibodies bind lipid A such that the GlcN-O6 attachment point for the core oligosaccharide is buried in the combining site, which explains the lack of LPS recognition. Longstanding reports of polyspecificity of anti-lipid A antibodies towards single stranded DNA combined with observed homology of S1-15 and A6 and the reports of several single stranded DNA-specific mAbs prompted the determination of the structure of S1-15 in complex with ssDNA fragments, which may provide clues into the genesis of autoimmune diseases such as systemic lupus erythematosus, thyroiditis, and rheumatic autoimmune diseases.
		+
		+	Structural Basis for Antibody Recognition of Lipid A: Insights to Polyspecificity Toward Single Stranded DNA.,Haji-Ghassemi O, Muller-Loennies S, Rodriguez T, Brade L, Kosma P, Brade H, Evans SV J Biol Chem. 2015 Jun 17. pii: jbc.M115.657874. PMID:26085093<ref>PMID:26085093</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4ods" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:16, 1 July 2015

OCA — Wed, 01 Jul 2015 12:16:59 GMT

←Older revision		Revision as of 12:16, 1 July 2015
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-	'''~~Unreleased structure~~'''	+	==Unliganded Fab structure of lipid A-specific antibody S55-3==
-		+	<StructureSection load='4ods' size='340' side='right' caption='[[4ods]], [[Resolution\|resolution]] 1.94Å' scene=''>
-	~~The entry~~ 4ods is ~~ON HOLD until Jul 10 2016~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ods]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ODS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ODS FirstGlance]. <br>
-	~~Authors~~: ~~Haji~~-~~Ghassemi~~, O., ~~Evans~~, S.V.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4odv\|4odv]], [[4odw\|4odw]], [[4ody\|4ody]], [[4odz\|4odz]], [[4oe0\|4oe0]]</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=4ods FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ods OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ods RCSB], [http://www.ebi.ac.uk/pdbsum/4ods PDBsum]</span></td></tr>
-	~~Description: Unliganded Fab structure of lipid A-specific antibody S55-3~~	+	</table>
-	[[Category: ~~Unreleased Structures~~]]	+	__TOC__
-	[[Category: Evans, S.V]]	+	</StructureSection>
		+	[[Category: Mus musculus]]
		+	[[Category: Evans, S V]]
	[[Category: Haji-Ghassemi, O]]		[[Category: Haji-Ghassemi, O]]
		+	[[Category: Carbohydrate binding]]
		+	[[Category: Immune system]]

OCA at 14:22, 24 December 2014

OCA — Wed, 24 Dec 2014 14:22:25 GMT

←Older revision		Revision as of 14:22, 24 December 2014
Line 6:		Line 6:

	Description: Unliganded Fab structure of lipid A-specific antibody S55-3		Description: Unliganded Fab structure of lipid A-specific antibody S55-3
		+	[[Category: Unreleased Structures]]
		+	[[Category: Evans, S.V]]
		+	[[Category: Haji-Ghassemi, O]]

OCA at 13:02, 10 December 2014

OCA — Wed, 10 Dec 2014 13:02:56 GMT

←Older revision		Revision as of 13:02, 10 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ods is ON HOLD until ~~Paper Publication~~	+	The entry 4ods is ON HOLD until Jul 10 2016

	Authors: Haji-Ghassemi, O., Evans, S.V.		Authors: Haji-Ghassemi, O., Evans, S.V.

	Description: Unliganded Fab structure of lipid A-specific antibody S55-3		Description: Unliganded Fab structure of lipid A-specific antibody S55-3

OCA at 07:37, 7 May 2014

OCA — Wed, 07 May 2014 07:37:24 GMT

←Older revision		Revision as of 07:37, 7 May 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ods is ON HOLD	+	The entry 4ods is ON HOLD until Paper Publication

	Authors: Haji-Ghassemi, O., Evans, S.V.		Authors: Haji-Ghassemi, O., Evans, S.V.

	Description: Unliganded Fab structure of lipid A-specific antibody S55-3		Description: Unliganded Fab structure of lipid A-specific antibody S55-3

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

OCA — Wed, 22 Jan 2014 06:47:32 GMT

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

←Older revision

Revision as of 06:47, 22 January 2014