2ywz - Revision history

OCA at 09:09, 25 October 2023

OCA — Wed, 25 Oct 2023 09:09:33 GMT

←Older revision		Revision as of 09:09, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2ywz' size='340' side='right'caption='[[2ywz]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='2ywz' size='340' side='right'caption='[[2ywz]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[1ver\|1ver]]~~, [[~~1ves~~\|~~1ves]], [[2coq\|2coq]], [[2ywy\|2ywy~~]]</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]] 2.21Å</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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [~~http~~://pdbe.org/2ywz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ywz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ywz 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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [https://pdbe.org/2ywz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [https://www.ebi.ac.uk/pdbsum/2ywz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ywz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A9CBG5_9CHON A9CBG5_9CHON]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Orectolobus maculatus]]		[[Category: Orectolobus maculatus]]
-	[[Category: Streltsov~~, V A]]~~	+	[[Category: Streltsov VA]]
-	~~[[Category: 1-a-11]]~~	+
-	~~[[Category: Ig vnar]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 13:06, 22 July 2020

OCA — Wed, 22 Jul 2020 13:06:47 GMT

←Older revision		Revision as of 13:06, 22 July 2020
Line 1:		Line 1:

	==Structure of new antigen receptor variable domain from sharks==		==Structure of new antigen receptor variable domain from sharks==
-	<StructureSection load='2ywz' size='340' side='right' caption='[[2ywz]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='2ywz' size='340' side='right'caption='[[2ywz]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://pdbe.org/2ywz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ywz 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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://pdbe.org/2ywz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ywz ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Orectolobus maculatus]]		[[Category: Orectolobus maculatus]]
	[[Category: Streltsov, V A]]		[[Category: Streltsov, V A]]

OCA at 08:46, 17 October 2018

OCA — Wed, 17 Oct 2018 08:46:56 GMT

←Older revision		Revision as of 08:46, 17 October 2018
Line 1:		Line 1:
		+
	==Structure of new antigen receptor variable domain from sharks==		==Structure of new antigen receptor variable domain from sharks==
	<StructureSection load='2ywz' size='340' side='right' caption='[[2ywz]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='2ywz' size='340' side='right' caption='[[2ywz]], [[Resolution\|resolution]] 2.21Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://pdbe.org/2ywz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz 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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://pdbe.org/2ywz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ywz ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yw/2ywz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yw/2ywz_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 12:22, 8 February 2016

OCA — Mon, 08 Feb 2016 12:22:43 GMT

←Older revision		Revision as of 12:22, 8 February 2016
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz 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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://pdbe.org/2ywz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ywz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 24:
	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 2ywz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:55, 20 January 2015

OCA — Tue, 20 Jan 2015 09:55:06 GMT

←Older revision		Revision as of 09:55, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz 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=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Orectolobus maculatus]]		[[Category: Orectolobus maculatus]]
-	[[Category: Streltsov, V A.]]	+	[[Category: Streltsov, V A]]
	[[Category: 1-a-11]]		[[Category: 1-a-11]]
	[[Category: Ig vnar]]		[[Category: Ig vnar]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 04:44, 2 October 2014

OCA — Thu, 02 Oct 2014 04:44:39 GMT

←Older revision		Revision as of 04:44, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2ywz.~~png~~\|~~left~~\|200px]]	+	==Structure of new antigen receptor variable domain from sharks==
		+	<StructureSection load='2ywz' size='340' side='right' caption='[[2ywz]], [[Resolution\|resolution]] 2.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YWZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ver\|1ver]], [[1ves\|1ves]], [[2coq\|2coq]], [[2ywy\|2ywy]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ywz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ywz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ywz RCSB], [http://www.ebi.ac.uk/pdbsum/2ywz PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yw/2ywz_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mimotopes mimic the three-dimensional topology of an antigen epitope, and are frequently recognized by antibodies with affinities comparable to those obtained for the original antibody-antigen interaction. Peptides and anti-idiotypic antibodies are two classes of protein mimotopes that mimic the topology (but not necessarily the sequence) of the parental antigen. In this study, we combine these two classes by selecting mimotopes based on single domain IgNAR antibodies, which display exceptionally long CDR3 loop regions (analogous to a constrained peptide library) presented in the context of an immunoglobulin framework with adjacent and supporting CDR1 loops. By screening an in vitro phage-display library of IgNAR variable domains (V(NAR)s) against the target antigen monoclonal antibody MAb5G8, we obtained four potential mimotopes. MAb5G8 targets a linear tripeptide epitope (AYP) in the flexible signal sequence of the Plasmodium falciparum Apical Membrane Antigen-1 (AMA1), and this or similar motifs were detected in the CDR loops of all four V(NAR)s. The V(NAR)s, 1-A-2, -7, -11, and -14, were demonstrated to bind specifically to this paratope by competition studies with an artificial peptide and all showed enhanced affinities (3-46 nM) compared to the parental antigen (175 nM). Crystallographic studies of recombinant proteins 1-A-7 and 1-A-11 showed that the SYP motifs on these V(NAR)s presented at the tip of the exposed CDR3 loops, ideally positioned within bulge-like structures to make contact with the MAb5G8 antibody. These loops, in particular in 1-A-11, were further stabilized by inter- and intra- loop disulphide bridges, hydrogen bonds, electrostatic interactions, and aromatic residue packing. We rationalize the higher affinity of the V(NAR)s compared to the parental antigen by suggesting that adjacent CDR1 and framework residues contribute to binding affinity, through interactions with other CDR regions on the antibody, though of course definitive support of this hypothesis will rely on co-crystallographic studies. Alternatively, the selection of mimotopes from a large (<4 x 10(8)) constrained library may have allowed selection of variants with even more favorable epitope topologies than present in the original antigenic structure, illustrating the power of in vivo selection of mimotopes from phage-displayed molecular libraries. Proteins 2008. (c) 2007 Wiley-Liss, Inc.

-	~~{{STRUCTURE_2ywz\| PDB=2ywz \| SCENE= }}~~	+	Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures.,Simmons DP, Streltsov VA, Dolezal O, Hudson PJ, Coley AM, Foley M, Proll DF, Nuttall SD Proteins. 2007 Oct 11;71(1):119-130. PMID:17932913<ref>PMID:17932913</ref>

-	~~===Structure~~ of ~~new antigen receptor variable domain from sharks===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17932913}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2ywz]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Orectolobus_maculatus Orectolobus maculatus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017932913<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Orectolobus maculatus]]		[[Category: Orectolobus maculatus]]
	[[Category: Streltsov, V A.]]		[[Category: Streltsov, V A.]]

OCA: Protected "2ywz" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:09:58 GMT

Protected "2ywz" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:09, 7 January 2013

OCA at 19:09, 7 January 2013

OCA — Mon, 07 Jan 2013 19:09:54 GMT

←Older revision		Revision as of 19:09, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ywz.png\|left\|200px]]		[[Image:2ywz.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2ywz\| PDB=2ywz \| SCENE= }}		{{STRUCTURE_2ywz\| PDB=2ywz \| SCENE= }}

	===Structure of new antigen receptor variable domain from sharks===		===Structure of new antigen receptor variable domain from sharks===

-
-	<!--
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	{{ABSTRACT_PUBMED_17932913}}		{{ABSTRACT_PUBMED_17932913}}

	==About this Structure==		==About this Structure==
-	~~2YWZ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA].	+	[[2ywz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17932913~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017932913</ref><references group="xtra"/>
	[[Category: Orectolobus maculatus]]		[[Category: Orectolobus maculatus]]
	[[Category: Streltsov, V A.]]		[[Category: Streltsov, V A.]]
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	[[Category: Ig vnar]]		[[Category: Ig vnar]]
	[[Category: Immune system]]		[[Category: Immune system]]
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-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:58:16 2009''

OCA at 19:58, 16 February 2009

OCA — Mon, 16 Feb 2009 19:58:17 GMT

←Older revision		Revision as of 19:58, 16 February 2009
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	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA].	+	2YWZ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Orectolobus_maculatus Orectolobus maculatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YWZ OCA].

	==Reference==		==Reference==
-	Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures., Simmons DP, Streltsov VA, Dolezal O, Hudson PJ, Coley AM, Foley M, Proll DF, Nuttall SD, Proteins. 2007 Oct 11;71(1):119-130. PMID:[~~http~~:~~//www.ncbi.nlm.nih.gov/pubmed/17932913 17932913~~]	+	<ref group="xtra">PMID:17932913</ref><references group="xtra"/>
		+	[[Category: Orectolobus maculatus]]
	[[Category: Streltsov, V A.]]		[[Category: Streltsov, V A.]]
	[[Category: 1-a-11]]		[[Category: 1-a-11]]
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	[[Category: Immune system]]		[[Category: Immune system]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 02~~:57:~~02 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:58:16 2009''

OCA at 23:57, 27 July 2008

OCA — Sun, 27 Jul 2008 23:57:10 GMT

←Older revision		Revision as of 23:57, 27 July 2008
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-	[[Image:2ywz.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2ywz.png\|left\|200px]]

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	{{STRUCTURE_2ywz\| PDB=2ywz \| SCENE= }}		{{STRUCTURE_2ywz\| PDB=2ywz \| SCENE= }}

-	~~'''~~Structure of new antigen receptor variable domain from sharks~~'''~~	+	===Structure of new antigen receptor variable domain from sharks===


-	~~==Overview==~~	+	<!--
-	~~Mimotopes mimic the three~~-~~dimensional topology of an antigen epitope, and are frequently recognized by antibodies with affinities comparable to those obtained for the original antibody~~-~~antigen interaction. Peptides and anti-idiotypic antibodies are two classes of protein mimotopes that mimic the topology (but not necessarily the sequence) of the parental antigen. In~~ this ~~study~~, ~~we combine these two classes by selecting mimotopes based on single domain IgNAR antibodies~~, ~~which display exceptionally long CDR3 loop regions (analogous to a constrained peptide library) presented in~~ the context of an immunoglobulin framework with adjacent and supporting CDR1 loops. By screening an in vitro phage-display library of IgNAR variable domains (V(NAR)s) against the target antigen monoclonal antibody MAb5G8, we obtained four potential mimotopes. MAb5G8 targets a linear tripeptide epitope (AYP) in the flexible signal sequence of the Plasmodium falciparum Apical Membrane Antigen-1 (AMA1), and this or similar motifs were detected in the CDR loops of all four V(NAR)s. The V(NAR)s, 1-A-2, -7, -11, and -14, were demonstrated to bind specifically to this paratope by competition studies with an artificial peptide and all showed enhanced affinities (3-46 nM) compared to the ~~parental antigen~~ (~~175 nM). Crystallographic studies of recombinant proteins 1-A-7 and 1-A-11 showed that the SYP motifs~~ on ~~these V(NAR)s presented~~ at ~~the tip of the exposed CDR3 loops, ideally positioned within bulge-like structures to make contact with the MAb5G8 antibody~~. ~~These loops, in particular in 1-A-11, were further stabilized by inter- and intra- loop disulphide bridges, hydrogen bonds, electrostatic interactions, and aromatic residue packing~~. ~~We rationalize the higher affinity of the V(NAR~~)~~s compared to the parental antigen by suggesting that adjacent CDR1 and framework residues contribute to binding affinity~~, ~~through interactions with other CDR regions on~~ the ~~antibody, though of course definitive support of this hypothesis will rely on co-crystallographic studies~~. Alternatively, the selection of mimotopes from a large (<4 x 10(8)) constrained library may have allowed selection of variants with even more favorable epitope topologies than present in the original antigenic structure, illustrating the power of in vivo selection of mimotopes from phage-~~displayed molecular libraries. Proteins 2008. (c) 2007 Wiley~~-~~Liss, Inc.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17932913}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17932913 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17932913}}

	==About this Structure==		==About this Structure==
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	[[Category: Ig vnar]]		[[Category: Ig vnar]]
	[[Category: Immune system]]		[[Category: Immune system]]
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