5c9k - Revision history

OCA at 08:36, 27 September 2023

OCA — Wed, 27 Sep 2023 08:36:06 GMT

←Older revision		Revision as of 08:36, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5c9k]] is a 8 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=5C9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C9K FirstGlance]. <br>		<table><tr><td colspan='2'>[[5c9k]] is a 8 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=5C9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C9K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.92Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [https://pdbe.org/5c9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [https://www.ebi.ac.uk/pdbsum/5c9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9k 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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [https://pdbe.org/5c9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [https://www.ebi.ac.uk/pdbsum/5c9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9k ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:25, 7 June 2023

OCA — Wed, 07 Jun 2023 06:25:29 GMT

←Older revision		Revision as of 06:25, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5c9k' size='340' side='right'caption='[[5c9k]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='5c9k' size='340' side='right'caption='[[5c9k]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c9k]] is a 8 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=5C9K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5C9K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c9k]] is a 8 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=5C9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C9K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b5g\|3b5g]], [[3bdx\|3bdx]]</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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [https://pdbe.org/5c9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [https://www.ebi.ac.uk/pdbsum/5c9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9k ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VL GENE SEGMENT 6A AND JL2/3 GENE SEGMENT ([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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [~~http~~://pdbe.org/5c9k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5c9k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9k ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q96JD1_HUMAN Q96JD1_HUMAN]
-	Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although lambda chains, particularly those belonging to the lambda6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the lambda6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wild-type protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced its capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the V(L) (variable region of the light chain)-V(L) interface. This mutant crystallized in two orthorhombic polymorphs, P2(1)2(1)2(1) and C222(1). In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222(1) lattice showed the establishment of intermolecular beta-beta interactions that involved the N-terminus and beta-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the V(L) interface in lambda6 LCs.	+
-		+
-	A single mutation at the sheet switch region results in conformational changes favoring lambda6 light-chain fibrillogenesis.,Hernandez-Santoyo A, del Pozo Yauner L, Fuentes-Silva D, Ortiz E, Rudino-Pinera E, Sanchez-Lopez R, Horjales E, Becerril B, Rodriguez-Romero A J Mol Biol. 2010 Feb 19;396(2):~~280-92. Epub 2009 Nov 24. PMID:19941869<ref>PMID:19941869<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5c9k" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Becerril-Lujan, B]]	+	[[Category: Becerril-Lujan B]]
-	[[Category: Hernandez-Santoyo, A]]	+	[[Category: Hernandez-Santoyo A]]
-	[[Category: Luna-Martinez~~, O D~~]]	+	[[Category: Luna-Martinez OD]]
-	[[Category: Rodriguez-Romero, A]]	+	[[Category: Rodriguez-Romero A]]
-	~~[[Category: Al amyloidosis]]~~	+
-	~~[[Category: Beta-sandwich]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin]]~~	+
-	~~[[Category: Lambda vi subgroup~~]]	+

OCA at 11:29, 27 March 2020

OCA — Fri, 27 Mar 2020 11:29:02 GMT

←Older revision		Revision as of 11:29, 27 March 2020
Line 1:		Line 1:

	==Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2==		==Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2==
-	<StructureSection load='5c9k' size='340' side='right' caption='[[5c9k]], [[Resolution\|resolution]] 1.92Å' scene=''>	+	<StructureSection load='5c9k' size='340' side='right'caption='[[5c9k]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c9k]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C9K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C9K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c9k]] is a 8 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=5C9K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C9K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b5g\|3b5g]], [[3bdx\|3bdx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b5g\|3b5g]], [[3bdx\|3bdx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VL GENE SEGMENT 6A AND JL2/3 GENE SEGMENT ([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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [http://pdbe.org/5c9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [http://www.ebi.ac.uk/pdbsum/5c9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9k 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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [http://pdbe.org/5c9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [http://www.ebi.ac.uk/pdbsum/5c9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9k ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Becerril-Lujan, B]]		[[Category: Becerril-Lujan, B]]
	[[Category: Hernandez-Santoyo, A]]		[[Category: Hernandez-Santoyo, A]]

OCA at 13:21, 10 May 2017

OCA — Wed, 10 May 2017 13:21:13 GMT

←Older revision		Revision as of 13:21, 10 May 2017
Line 1:		Line 1:
		+
	==Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2==		==Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2==
	<StructureSection load='5c9k' size='340' side='right' caption='[[5c9k]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='5c9k' size='340' side='right' caption='[[5c9k]], [[Resolution\|resolution]] 1.92Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b5g\|3b5g]], [[3bdx\|3bdx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b5g\|3b5g]], [[3bdx\|3bdx]]</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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [http://www.ebi.ac.uk/pdbsum/5c9k 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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [http://pdbe.org/5c9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [http://www.ebi.ac.uk/pdbsum/5c9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c9k 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 5c9k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:01, 5 August 2015

OCA — Wed, 05 Aug 2015 20:01:03 GMT

←Older revision		Revision as of 20:01, 5 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2==
		+	<StructureSection load='5c9k' size='340' side='right' caption='[[5c9k]], [[Resolution\|resolution]] 1.92Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5c9k]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C9K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C9K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b5g\|3b5g]], [[3bdx\|3bdx]]</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=5c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c9k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5c9k RCSB], [http://www.ebi.ac.uk/pdbsum/5c9k PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although lambda chains, particularly those belonging to the lambda6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the lambda6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wild-type protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced its capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the V(L) (variable region of the light chain)-V(L) interface. This mutant crystallized in two orthorhombic polymorphs, P2(1)2(1)2(1) and C222(1). In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222(1) lattice showed the establishment of intermolecular beta-beta interactions that involved the N-terminus and beta-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the V(L) interface in lambda6 LCs.

-	~~The entry 5c9k is ON HOLD~~	+	A single mutation at the sheet switch region results in conformational changes favoring lambda6 light-chain fibrillogenesis.,Hernandez-Santoyo A, del Pozo Yauner L, Fuentes-Silva D, Ortiz E, Rudino-Pinera E, Sanchez-Lopez R, Horjales E, Becerril B, Rodriguez-Romero A J Mol Biol. 2010 Feb 19;396(2):280-92. Epub 2009 Nov 24. PMID:19941869<ref>PMID:19941869</ref>

-	~~Authors: Hernandez-Santoyo~~, A.~~, Rodriguez-Romero, A~~.~~, Luna-Martinez, O.D., Becerril-Lujan, B~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of a highly fibrillogenic Arg25Gly mutant of the Recombinant variable domain 6AJL2~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Becerril-Lujan, B]]
	[[Category: Hernandez-Santoyo, A]]		[[Category: Hernandez-Santoyo, A]]
-	[[Category: ~~Becerril~~-~~Lujan~~, B]]	+	[[Category: Luna-Martinez, O D]]
	[[Category: Rodriguez-Romero, A]]		[[Category: Rodriguez-Romero, A]]
-	[[Category: ~~Luna~~-~~Martinez, O.D~~]]	+	[[Category: Al amyloidosis]]
		+	[[Category: Beta-sandwich]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin]]
		+	[[Category: Lambda vi subgroup]]

OCA: Protected "5c9k" [edit=sysop:move=sysop]

OCA — Wed, 08 Jul 2015 13:52:22 GMT

Protected "5c9k" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:52, 8 July 2015

OCA: New page: '''Unreleased structure''' The entry 5c9k is ON HOLD Authors: Hernandez-Santoyo, A., Rodriguez-Romero, A., Luna-Martinez, O.D., Becerril-Lujan, B. Description: Crystal structure of a h...

OCA — Wed, 08 Jul 2015 13:52:21 GMT

New page: '''Unreleased structure''' The entry 5c9k is ON HOLD Authors: Hernandez-Santoyo, A., Rodriguez-Romero, A., Luna-Martinez, O.D., Becerril-Lujan, B. Description: Crystal structure of a h...

New page

'''Unreleased structure'''

The entry 5c9k is ON HOLD

Authors: Hernandez-Santoyo, A., Rodriguez-Romero, A., Luna-Martinez, O.D., Becerril-Lujan, B.

Description: Crystal structure of a highly fibrillogenic Arg25Gly mutant of the Recombinant variable domain 6AJL2
[[Category: Unreleased Structures]]
[[Category: Hernandez-Santoyo, A]]
[[Category: Becerril-Lujan, B]]
[[Category: Rodriguez-Romero, A]]
[[Category: Luna-Martinez, O.D]]