1pew - Revision history

OCA at 09:42, 16 August 2023

OCA — Wed, 16 Aug 2023 09:42:09 GMT

←Older revision		Revision as of 09:42, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1pew' size='340' side='right'caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1pew' size='340' side='right'caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pew]] is a 2 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=1PEW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PEW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pew]] is a 2 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=1PEW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PEW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CD:CADMIUM+ION'>CD</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]] 1.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1cd0\|1cd0]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [https://pdbe.org/1pew PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [https://www.ebi.ac.uk/pdbsum/1pew PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pew 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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [~~http~~://pdbe.org/1pew PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pew PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pew ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LV657_HUMAN LV657_HUMAN] V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref> <ref>PMID:24600447</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dealwis, C]]	+	[[Category: Dealwis C]]
-	[[Category: Gupta, V]]	+	[[Category: Gupta V]]
-	[[Category: Wilkerson, M]]	+	[[Category: Wilkerson M]]
-	~~[[Category: Beta sheet]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 07:28, 9 December 2020

OCA — Wed, 09 Dec 2020 07:28:26 GMT

←Older revision		Revision as of 07:28, 9 December 2020
Line 1:		Line 1:

	==High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto==		==High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto==
-	<StructureSection load='1pew' size='340' side='right' caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1pew' size='340' side='right'caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pew]] is a 2 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=1PEW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PEW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pew]] is a 2 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=1PEW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PEW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cd0\|1cd0]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://pdbe.org/1pew PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pew 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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://pdbe.org/1pew PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pew ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]
	[[Category: Gupta, V]]		[[Category: Gupta, V]]

OCA at 08:03, 15 February 2018

OCA — Thu, 15 Feb 2018 08:03:50 GMT

←Older revision		Revision as of 08:03, 15 February 2018
Line 1:		Line 1:
		+
	==High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto==		==High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto==
	<StructureSection load='1pew' size='340' side='right' caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1pew' size='340' side='right' caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://pdbe.org/1pew PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew 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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://pdbe.org/1pew PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pew ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/1pew_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/1pew_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 21:53, 7 February 2016

OCA — Sun, 07 Feb 2016 21:53:40 GMT

←Older revision		Revision as of 21:53, 7 February 2016
Line 16:		Line 16:
	<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=1pew ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:17, 10 September 2015

OCA — Thu, 10 Sep 2015 05:17:16 GMT

←Older revision		Revision as of 05:17, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1pew' size='340' side='right' caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1pew' size='340' side='right' caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pew]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PEW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pew]] is a 2 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=1PEW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PEW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew 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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://pdbe.org/1pew PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1pew" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]
	[[Category: Gupta, V]]		[[Category: Gupta, V]]

OCA at 08:32, 6 January 2015

OCA — Tue, 06 Jan 2015 08:32:21 GMT

←Older revision		Revision as of 08:32, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pew]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PEW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pew]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PEW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew 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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew 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 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Dealwis, C.]]	+	[[Category: Dealwis, C]]
-	[[Category: Gupta, V.]]	+	[[Category: Gupta, V]]
-	[[Category: Wilkerson, M.]]	+	[[Category: Wilkerson, M]]
	[[Category: Beta sheet]]		[[Category: Beta sheet]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 20:43, 28 September 2014

OCA — Sun, 28 Sep 2014 20:43:26 GMT

←Older revision		Revision as of 20:43, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1pew.~~png~~\|~~left~~\|200px]]	+	==High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto==
		+	<StructureSection load='1pew' size='340' side='right' caption='[[1pew]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pew]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PEW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cd0\|1cd0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Jto ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=1pew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pew OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pew RCSB], [http://www.ebi.ac.uk/pdbsum/1pew 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/pe/1pew_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 ==
		+	Primary (AL) amyloidosis results from the pathologic deposition of monoclonal light chains as amyloid fibrils. Studies of recombinant-derived variable region (VL) fragments of these proteins have shown an inverse relationship between thermodynamic stability and fibrillogenic potential. Further, ionic interactions within the VL domain were predicted to influence the kinetics of light chain fibrillogenicity, as evidenced from our analyses of a relatively stable Vlambda6 protein (Jto) with a long range electrostatic interaction between Asp and Arg side chains at position 29 and 68, respectively, and an unstable, highly fibrillogenic Vlambda6 protein (Wil) that had neutral amino acids at these locations. To test this hypothesis, we have generated two Jto-related mutants designed to disrupt the interaction between Asp 29 and Arg 68 (JtoD29A and JtoR68S). Although the thermodynamic stabilities of unfolding for these two molecules were identical, they exhibited very different kinetics of fibril formation: the rate of JtoD29A fibrillogenesis was slow and comparable to the parent molecule, whereas that of JtoR68S was significantly faster. High-resolution X-ray diffraction analyses of crystals prepared from the two mutants having the same space group and unit cell dimensions revealed no significant main-chain conformational changes. However, several notable side-chain alterations were observed in JtoR68S, as compared with JtoD29A, that resulted in the solvent exposure of a greater hydrophobic surface and modifications in the electrostatic potential surface. We posit that these differences contributed to the enhanced fibrillogenic potential of the Arg 68 mutant, since both Jto mutants lacked the intrachain ionic interaction and were equivalently unstable. The information gleaned from our studies has provided insight into structural parameters that in addition to overall thermodynamic stability, contribute to the fibril forming propensity of immunoglobulin light chains.

-	~~{{STRUCTURE_1pew\| PDB=1pew \| SCENE= }}~~	+	Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four Vlambda6 proteins.,Wall JS, Gupta V, Wilkerson M, Schell M, Loris R, Adams P, Solomon A, Stevens F, Dealwis C J Mol Recognit. 2004 Jul-Aug;17(4):323-31. PMID:15227639<ref>PMID:15227639</ref>

-	~~===High Resolution Crystal Structure of Jto2~~, a ~~mutant~~ of the ~~non-amyloidogenic Lamba6 Light Chain, Jto===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15227639}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1pew]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015227639<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Dealwis, C.]]		[[Category: Dealwis, C.]]

OCA: Protected "1pew" [edit=sysop:move=sysop]

OCA — Wed, 19 Dec 2012 12:12:56 GMT

Protected "1pew" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:12, 19 December 2012

OCA at 12:12, 19 December 2012

OCA — Wed, 19 Dec 2012 12:12:53 GMT

←Older revision		Revision as of 12:12, 19 December 2012
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-	{{Seed}}
	[[Image:1pew.png\|left\|200px]]		[[Image:1pew.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pew", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1pew\| PDB=1pew \| SCENE= }}		{{STRUCTURE_1pew\| PDB=1pew \| SCENE= }}

	===High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto===		===High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15227639}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15227639 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15227639}}		{{ABSTRACT_PUBMED_15227639}}

	==About this Structure==		==About this Structure==
-	~~1PEW~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA].	+	[[1pew]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15227639~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015227639</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Dealwis, C.]]		[[Category: Dealwis, C.]]
Line 29:		Line 17:
	[[Category: Wilkerson, M.]]		[[Category: Wilkerson, M.]]
	[[Category: Beta sheet]]		[[Category: Beta sheet]]
-		+	[[Category: Immune system]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 16:45:08 2009''~~	+

OCA at 14:45, 16 February 2009

OCA — Mon, 16 Feb 2009 14:45:08 GMT

←Older revision		Revision as of 14:45, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1PEW is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA].	+	1PEW is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEW OCA].

	==Reference==		==Reference==
-	Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four Vlambda6 proteins., Wall JS, Gupta V, Wilkerson M, Schell M, Loris R, Adams P, Solomon A, Stevens F, Dealwis C, J Mol Recognit. 2004 Jul-Aug;17(4):323-31. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15227639 15227639]~~	+	<ref group="xtra">PMID:15227639</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Single protein]]
	[[Category: Dealwis, C.]]		[[Category: Dealwis, C.]]
	[[Category: Gupta, V.]]		[[Category: Gupta, V.]]
Line 31:		Line 30:
	[[Category: Beta sheet]]		[[Category: Beta sheet]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 19~~:59:~~38 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:45:08 2009''