5sv4 - Revision history

OCA at 12:48, 4 October 2023

2023-10-04T12:48:18Z

←Older revision		Revision as of 12:48, 4 October 2023
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	<StructureSection load='5sv4' size='340' side='right'caption='[[5sv4]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5sv4' size='340' side='right'caption='[[5sv4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5sv4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Camelus_glama Camelus~~ glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SV4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5SV4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5sv4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SV4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5sv3\|5sv3]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5sv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sv4 OCA], [~~http~~://pdbe.org/5sv4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5sv4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5sv4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5sv4 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=5sv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sv4 OCA], [https://pdbe.org/5sv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sv4 RCSB], [https://www.ebi.ac.uk/pdbsum/5sv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sv4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Camelus~~ glama]]	+	[[Category: Lama glama]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Compton~~, J R~~]]	+	[[Category: Compton JR]]
-	[[Category: Legler~~, P M]]~~	+	[[Category: Legler PM]]
-	~~[[Category: A-chain]]~~	+
-	~~[[Category: Ricin]]~~	+
-	~~[[Category: Sdab]]~~	+
-	~~[[Category: Single domain antibody]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 09:02, 1 January 2020

2020-01-01T09:02:59Z

←Older revision		Revision as of 09:02, 1 January 2020
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	==Anti-Ricin A-chain Single Domain Antibody A3C8==		==Anti-Ricin A-chain Single Domain Antibody A3C8==
-	<StructureSection load='5sv4' size='340' side='right' caption='[[5sv4]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5sv4' size='340' side='right'caption='[[5sv4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5sv4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SV4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5sv4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SV4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5sv3\|5sv3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5sv3\|5sv3]]</td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5sv4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5sv4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Camelus glama]]
		+	[[Category: Large Structures]]
	[[Category: Compton, J R]]		[[Category: Compton, J R]]
	[[Category: Legler, P M]]		[[Category: Legler, P M]]

OCA at 17:30, 19 October 2016

2016-10-19T17:30:47Z

←Older revision		Revision as of 17:30, 19 October 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5sv4 is ~~ON HOLD~~	+	==Anti-Ricin A-chain Single Domain Antibody A3C8==
		+	<StructureSection load='5sv4' size='340' side='right' caption='[[5sv4]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5sv4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SV4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5sv3\|5sv3]]</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=5sv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sv4 OCA], [http://pdbe.org/5sv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sv4 RCSB], [http://www.ebi.ac.uk/pdbsum/5sv4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sv4 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ricin is an A-B ribosome inactivating protein (RIP) toxin composed of an A-chain subunit (RTA) that contains a catalytic N-glycosidase and a B-chain (RTB) lectin domain that binds cell surface glycans. Ricin exploits retrograde transport to enter into the Golgi and the endoplasmic reticulum, and then dislocates into the cytoplasm where it can reach its substrate, the ribosomal RNA. A subset of isolated antibodies (Abs) raised against the RTA subunit protect against ricin intoxication, and RTA-based vaccine immunogens have been shown to provide long-lasting protective immunity against the holotoxin. Anti-RTA Abs are unlikely to cross a membrane and reach the cytoplasm to inhibit the enzymatic activity of the A-chain. Moreover, there is not a strict correlation between the apparent binding affinity (Ka) of anti-RTA Abs and their ability to successfully neutralize ricin toxicity. Some anti-RTA antibodies are toxin-neutralizing, whereas others are not. We hypothesize that neutralizing anti-RTA Abs may interfere selectively with conformational change(s) or partial unfolding required for toxin internalization. To test this hypothesis, we measured the melting temperatures (Tm) of neutralizing single-domain Ab (sdAb)-antigen (Ag) complexes relative to the Tm of the free antigen (Tm-shift = Tmcomplex - TmAg), and observed increases in the Tmcomplex of 9-20 degrees. In contrast, non-neutralizing sdAb-Ag complexes shifted the TmComplex by only 6-7 degrees. A strong linear correlation (r2 = 0.992) was observed between the magnitude of the Tm-shift and the viability of living cells treated with the sdAb and ricin holotoxin. The Tm-shift of the sdAb-Ag complex provided a quantitative biophysical parameter that could be used to predict and rank-order the toxin-neutralizing activities of Abs. We determined the first structure of an sdAb-RTA1-33/44-198 complex, and examined other sdAb-RTA complexes. We found that neutralizing sdAb bound to regions involved in the early stages of unfolding. These Abs likely interfere with steps preceding or following endocytosis that require conformational changes. This method may have utility for the characterization or rapid screening of other Ab that act to prevent conformational changes or unfolding as part of their mechanism of action.

-	~~Authors: Compton, J.R~~., Legler, P.M.	+	Stability of isolated antibody-antigen complexes as a predictive tool for selecting toxin neutralizing antibodies.,Legler PM, Compton JR, Hale ML, Anderson GP, Olson MA, Millard CB, Goldman ER MAbs. 2016 Sep 23:0. PMID:27660893<ref>PMID:27660893</ref>

-	~~Description: Anti~~-~~Ricin A~~-~~chain Single Domain Antibody A3C8~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Legler, P.M]]	+	<div class="pdbe-citations 5sv4" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Compton, J.R~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Compton, J R]]
		+	[[Category: Legler, P M]]
		+	[[Category: A-chain]]
		+	[[Category: Ricin]]
		+	[[Category: Sdab]]
		+	[[Category: Single domain antibody]]
		+	[[Category: Toxin]]

OCA: Protected "5sv4" [edit=sysop:move=sysop]

2016-08-10T14:43:59Z

Protected "5sv4" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:43, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5sv4 is ON HOLD Authors: Compton, J.R., Legler, P.M. Description: Anti-Ricin A-chain Single Domain Antibody A3C8 [[Category: Unreleased Structures]...

2016-08-10T14:43:58Z

New page: '''Unreleased structure''' The entry 5sv4 is ON HOLD Authors: Compton, J.R., Legler, P.M. Description: Anti-Ricin A-chain Single Domain Antibody A3C8 [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 5sv4 is ON HOLD

Authors: Compton, J.R., Legler, P.M.

Description: Anti-Ricin A-chain Single Domain Antibody A3C8
[[Category: Unreleased Structures]]
[[Category: Legler, P.M]]
[[Category: Compton, J.R]]