4z8f - Revision history

OCA at 08:13, 27 September 2023

2023-09-27T08:13:47Z

←Older revision		Revision as of 08:13, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4z8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4z8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z8F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</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]] 1.75Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [https://pdbe.org/4z8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [https://www.ebi.ac.uk/pdbsum/4z8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8f 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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [https://pdbe.org/4z8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [https://www.ebi.ac.uk/pdbsum/4z8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8f ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:43, 10 May 2023

2023-05-10T07:43:24Z

←Older revision		Revision as of 07:43, 10 May 2023
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	<StructureSection load='4z8f' size='340' side='right'caption='[[4z8f]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4z8f' size='340' side='right'caption='[[4z8f]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4z8f]] is a 4 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=4Z8F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Z8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4z8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z8F FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4z95\|4z95]]~~</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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [https://pdbe.org/4z8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [https://www.ebi.ac.uk/pdbsum/4z8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8f 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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [~~http~~://pdbe.org/4z8f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4z8f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8f 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: Synthetic construct]]
-	[[Category: ~~Haji-Ghassemi, O~~]]	+	[[Category: Evans SV]]
-	[[Category: ~~Antibody]]~~	+	[[Category: Haji-Ghassemi O]]
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Immune system~~-~~dna complex]]~~	+
-	~~[[Category: Lipid some~~]]	+

OCA at 07:53, 8 January 2020

2020-01-08T07:53:07Z

←Older revision		Revision as of 07:53, 8 January 2020
Line 1:		Line 1:

	==Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'==		==Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'==
-	<StructureSection load='4z8f' size='340' side='right' caption='[[4z8f]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='4z8f' size='340' side='right'caption='[[4z8f]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4z8f]] is a 4 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=4Z8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4z8f]] is a 4 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=4Z8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z8F FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Evans, S V]]		[[Category: Evans, S V]]

OCA at 12:20, 6 November 2017

2017-11-06T12:20:27Z

←Older revision		Revision as of 12:20, 6 November 2017
Line 1:		Line 1:
		+
	==Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'==		==Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'==
	<StructureSection load='4z8f' size='340' side='right' caption='[[4z8f]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4z8f' size='340' side='right' caption='[[4z8f]], [[Resolution\|resolution]] 1.75Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4z95\|4z95]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4z95\|4z95]]</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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [http://www.ebi.ac.uk/pdbsum/4z8f 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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [http://pdbe.org/4z8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [http://www.ebi.ac.uk/pdbsum/4z8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z8f ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4z8f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:09, 1 July 2015

2015-07-01T12:09:31Z

←Older revision		Revision as of 12:09, 1 July 2015
Line 7:		Line 7:
	<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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [http://www.ebi.ac.uk/pdbsum/4z8f 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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [http://www.ebi.ac.uk/pdbsum/4z8f 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>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:04, 24 June 2015

2015-06-24T13:04:27Z

←Older revision		Revision as of 13:04, 24 June 2015
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	==Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'==
-		+	<StructureSection load='4z8f' size='340' side='right' caption='[[4z8f]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	~~The entry 4z8f is ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4z8f]] is a 4 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=4Z8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z8F FirstGlance]. <br>
-	~~Authors: Haji-Ghassemi, O., Evans, S.V.~~	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4odt\|4odt]], [[4odu\|4odu]], [[4z95\|4z95]]</td></tr>
-	~~Description:~~ Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'	+	<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=4z8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4z8f RCSB], [http://www.ebi.ac.uk/pdbsum/4z8f PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Evans, S.V]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Mus musculus]]
		+	[[Category: Evans, S V]]
	[[Category: Haji-Ghassemi, O]]		[[Category: Haji-Ghassemi, O]]
		+	[[Category: Antibody]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Dna]]
		+	[[Category: Fab]]
		+	[[Category: Immune system-dna complex]]
		+	[[Category: Lipid some]]

OCA at 11:29, 6 May 2015

2015-05-06T11:29:22Z

←Older revision		Revision as of 11:29, 6 May 2015
Line 3:		Line 3:
	The entry 4z8f is ON HOLD		The entry 4z8f is ON HOLD

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

	Description: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'		Description: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Haji-Ghassemi, O~~, Evans, Sv~~]]	+	[[Category: Evans, S.V]]
		+	[[Category: Haji-Ghassemi, O]]

OCA: Protected "4z8f" [edit=sysop:move=sysop]

2015-04-15T11:48:25Z

Protected "4z8f" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:48, 15 April 2015

OCA: New page: '''Unreleased structure''' The entry 4z8f is ON HOLD Authors: Haji-Ghassemi, O, Evans, SV Description: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3' [[Catego...

2015-04-15T11:48:23Z

New page: '''Unreleased structure''' The entry 4z8f is ON HOLD Authors: Haji-Ghassemi, O, Evans, SV Description: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3' [[Catego...

New page

'''Unreleased structure'''

The entry 4z8f is ON HOLD

Authors: Haji-Ghassemi, O, Evans, SV

Description: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'
[[Category: Unreleased Structures]]
[[Category: Haji-Ghassemi, O, Evans, Sv]]