3rfs - Revision history

OCA at 06:01, 15 June 2022

OCA — Wed, 15 Jun 2022 06:01:30 GMT

←Older revision		Revision as of 06:01, 15 June 2022
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	<StructureSection load='3rfs' size='340' side='right'caption='[[3rfs]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3rfs' size='340' side='right'caption='[[3rfs]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rfs]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lism2 Lism2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RFS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rfs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lism2 Lism2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RFS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rfj\|3rfj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rfj\|3rfj]]</div></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=3rfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfs OCA], [~~http~~://pdbe.org/3rfs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rfs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rfs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rfs 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=3rfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfs OCA], [https://pdbe.org/3rfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rfs RCSB], [https://www.ebi.ac.uk/pdbsum/3rfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rfs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:22, 28 August 2019

OCA — Wed, 28 Aug 2019 16:22:21 GMT

←Older revision		Revision as of 16:22, 28 August 2019
Line 1:		Line 1:

	==Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering==		==Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering==
-	<StructureSection load='3rfs' size='340' side='right' caption='[[3rfs]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='3rfs' size='340' side='right'caption='[[3rfs]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rfs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lism2 Lism2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RFS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rfs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lism2 Lism2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RFS FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lism2]]		[[Category: Lism2]]
	[[Category: Cheong, H K]]		[[Category: Cheong, H K]]

OCA at 08:14, 11 August 2016

OCA — Thu, 11 Aug 2016 08:14:52 GMT

←Older revision		Revision as of 08:14, 11 August 2016
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		+
	==Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering==		==Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering==
	<StructureSection load='3rfs' size='340' side='right' caption='[[3rfs]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3rfs' size='340' side='right' caption='[[3rfs]], [[Resolution\|resolution]] 1.70Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rfj\|3rfj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rfj\|3rfj]]</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=3rfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rfs RCSB], [http://www.ebi.ac.uk/pdbsum/3rfs 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=3rfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfs OCA], [http://pdbe.org/3rfs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rfs RCSB], [http://www.ebi.ac.uk/pdbsum/3rfs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rfs 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 3rfs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:22, 4 January 2015

OCA — Sun, 04 Jan 2015 10:22:12 GMT

←Older revision		Revision as of 10:22, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rfs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lism2 Lism2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RFS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rfs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lism2 Lism2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RFS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rfj\|3rfj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rfj\|3rfj]]</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=3rfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rfs RCSB], [http://www.ebi.ac.uk/pdbsum/3rfs 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=3rfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rfs RCSB], [http://www.ebi.ac.uk/pdbsum/3rfs PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 13:
	Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering.,Lee SC, Park K, Han J, Lee JJ, Kim HJ, Hong S, Heu W, Kim YJ, Ha JS, Lee SG, Cheong HK, Jeon YH, Kim D, Kim HS Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3299-304. Epub 2012 Feb 10. PMID:22328160<ref>PMID:22328160</ref>		Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering.,Lee SC, Park K, Han J, Lee JJ, Kim HJ, Hong S, Heu W, Kim YJ, Ha JS, Lee SG, Cheong HK, Jeon YH, Kim D, Kim HS Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3299-304. Epub 2012 Feb 10. PMID:22328160<ref>PMID:22328160</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Lism2]]		[[Category: Lism2]]
-	[[Category: Cheong, H K.]]	+	[[Category: Cheong, H K]]
-	[[Category: Jeon, Y H.]]	+	[[Category: Jeon, Y H]]
-	[[Category: Kim, H J.]]	+	[[Category: Kim, H J]]
	[[Category: Lrr]]		[[Category: Lrr]]
	[[Category: Plasma]]		[[Category: Plasma]]
	[[Category: Protein binding]]		[[Category: Protein binding]]

OCA at 04:45, 5 June 2014

OCA — Thu, 05 Jun 2014 04:45:33 GMT

←Older revision		Revision as of 04:45, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3rfs.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering==
		+	<StructureSection load='3rfs' size='340' side='right' caption='[[3rfs]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rfs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lism2 Lism2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RFS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rfj\|3rfj]]</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=3rfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rfs RCSB], [http://www.ebi.ac.uk/pdbsum/3rfs PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Repeat proteins have recently been of great interest as potential alternatives to immunoglobulin antibodies due to their unique structural and biophysical features. We here present the development of a binding scaffold based on variable lymphocyte receptors, which are nonimmunoglobulin antibodies composed of Leucine-rich repeat modules in jawless vertebrates, by module engineering. A template scaffold was first constructed by joining consensus repeat modules between the N- and C-capping motifs of variable lymphocyte receptors. The N-terminal domain of the template scaffold was redesigned based on the internalin-B cap by analyzing the modular similarity between the respective repeat units using a computational approach. The newly designed scaffold, termed "Repebody," showed a high level of soluble expression in bacteria, displaying high thermodynamic and pH stabilities. Ease of molecular engineering was shown by designing repebodies specific for myeloid differentiation protein-2 and hen egg lysozyme, respectively, by a rational approach. The crystal structures of designed repebodies were determined to elucidate the structural features and interaction interfaces. We demonstrate general applicability of the scaffold by selecting repebodies with different binding affinities for interleukin-6 using phage display.

-	~~<!--~~	+	Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering.,Lee SC, Park K, Han J, Lee JJ, Kim HJ, Hong S, Heu W, Kim YJ, Ha JS, Lee SG, Cheong HK, Jeon YH, Kim D, Kim HS Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3299-304. Epub 2012 Feb 10. PMID:22328160<ref>PMID:22328160</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3rfs"~~, ~~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_3rfs\| PDB=3rfs \| SCENE= }}~~	+

-	~~===Design of~~ a ~~binding scaffold based on variable lymphocyte receptors~~ of ~~jawless vertebrates by module engineering===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22328160}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22328160 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+	[[Category: Lism2]]
-	~~{{ABSTRACT_PUBMED_22328160}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3rfs]] is a 2 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Listeria_monocytogenes,_synthetic,_eptatretus_burgeri Listeria monocytogenes, synthetic, eptatretus burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022328160<~~/~~ref~~><~~references group="xtra"~~/>	+
-	[[Category: ~~Listeria monocytogenes, synthetic, eptatretus burgeri~~]]	+
	[[Category: Cheong, H K.]]		[[Category: Cheong, H K.]]
	[[Category: Jeon, Y H.]]		[[Category: Jeon, Y H.]]

OCA at 06:36, 14 March 2012

OCA — Wed, 14 Mar 2012 06:36:50 GMT

←Older revision		Revision as of 06:36, 14 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rfs.jpg\|left\|200px]]

-	The ~~entry 3rfs~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rfs", 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_3rfs\| PDB=3rfs \| SCENE= }}

-	~~Authors: Kim, H.J., Cheong, H.K., Jeon, Y.H.~~	+	===Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering===

-	~~Description~~: ~~Design of~~ a binding ~~scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22328160}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22328160 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22328160}}
		+
		+	==About this Structure==
		+	[[3rfs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes,_synthetic,_eptatretus_burgeri Listeria monocytogenes, synthetic, eptatretus burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFS OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022328160</ref><references group="xtra"/>
		+	[[Category: Listeria monocytogenes, synthetic, eptatretus burgeri]]
		+	[[Category: Cheong, H K.]]
		+	[[Category: Jeon, Y H.]]
		+	[[Category: Kim, H J.]]
		+	[[Category: Lrr]]
		+	[[Category: Plasma]]
		+	[[Category: Protein binding]]

OCA at 05:26, 10 August 2011

OCA — Wed, 10 Aug 2011 05:26:13 GMT

←Older revision		Revision as of 05:26, 10 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rfs is ON HOLD	+	The entry 3rfs is ON HOLD until Paper Publication

	Authors: Kim, H.J., Cheong, H.K., Jeon, Y.H.		Authors: Kim, H.J., Cheong, H.K., Jeon, Y.H.

	Description: Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering		Description: Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

OCA at 05:50, 15 June 2011

OCA — Wed, 15 Jun 2011 05:50:49 GMT

←Older revision		Revision as of 05:50, 15 June 2011
Line 3:		Line 3:
	The entry 3rfs is ON HOLD		The entry 3rfs is ON HOLD

-	Authors: Kim, H.J. , Cheong, H.K. , Jeon, Y.H.	+	Authors: Kim, H.J., Cheong, H.K., Jeon, Y.H.

	Description: Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering		Description: Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

OCA: Protected "3rfs" [edit=sysop:move=sysop]

OCA — Wed, 13 Apr 2011 05:01:08 GMT

Protected "3rfs" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:01, 13 April 2011

OCA: New page: '''Unreleased structure''' The entry 3rfs is ON HOLD Authors: Kim, H.J. , Cheong, H.K. , Jeon, Y.H. Description: Design of a binding scaffold based on variable lymphocyte receptors of ...

OCA — Wed, 13 Apr 2011 05:01:07 GMT

New page: '''Unreleased structure''' The entry 3rfs is ON HOLD Authors: Kim, H.J. , Cheong, H.K. , Jeon, Y.H. Description: Design of a binding scaffold based on variable lymphocyte receptors of ...

New page

'''Unreleased structure'''

The entry 3rfs is ON HOLD

Authors: Kim, H.J. , Cheong, H.K. , Jeon, Y.H.

Description: Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering