3zhl - Revision history

OCA at 05:46, 10 August 2022

OCA — Wed, 10 Aug 2022 05:46:51 GMT

←Older revision		Revision as of 05:46, 10 August 2022
Line 1:		Line 1:

	==The crystal structure of single domain antibody 8-14 scaffold==		==The crystal structure of single domain antibody 8-14 scaffold==
-	<StructureSection load='3zhl' size='340' side='right' caption='[[3zhl]], [[Resolution\|resolution]] 2.47Å' scene=''>	+	<StructureSection load='3zhl' size='340' side='right'caption='[[3zhl]], [[Resolution\|resolution]] 2.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zhl]] is a 1 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=3ZHL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zhl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhd\|3zhd]], [[3zhk\|3zhk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zhd\|3zhd]], [[3zhk\|3zhk]]</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=3zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhl OCA], [~~http~~://pdbe.org/3zhl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zhl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zhl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhl 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=3zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhl OCA], [https://pdbe.org/3zhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhl RCSB], [https://www.ebi.ac.uk/pdbsum/3zhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Lim, H K]]		[[Category: Lim, H K]]
	[[Category: Song, H N]]		[[Category: Song, H N]]

OCA at 16:39, 27 February 2019

OCA — Wed, 27 Feb 2019 16:39:12 GMT

←Older revision		Revision as of 16:39, 27 February 2019
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[3D structures ~~of antibody~~\|3D structures ~~of antibody~~]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:12, 11 August 2016

OCA — Thu, 11 Aug 2016 10:12:24 GMT

←Older revision		Revision as of 10:12, 11 August 2016
Line 1:		Line 1:
		+
	==The crystal structure of single domain antibody 8-14 scaffold==		==The crystal structure of single domain antibody 8-14 scaffold==
	<StructureSection load='3zhl' size='340' side='right' caption='[[3zhl]], [[Resolution\|resolution]] 2.47Å' scene=''>		<StructureSection load='3zhl' size='340' side='right' caption='[[3zhl]], [[Resolution\|resolution]] 2.47Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhd\|3zhd]], [[3zhk\|3zhk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhd\|3zhd]], [[3zhk\|3zhk]]</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=3zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhl RCSB], [http://www.ebi.ac.uk/pdbsum/3zhl 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=3zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhl OCA], [http://pdbe.org/3zhl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zhl RCSB], [http://www.ebi.ac.uk/pdbsum/3zhl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhl 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 3zhl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[~~Antibody~~\|~~Antibody~~]]	+	*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:45, 5 January 2015

OCA — Mon, 05 Jan 2015 12:45:45 GMT

←Older revision		Revision as of 12:45, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3zhl]] is a 1 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=3ZHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHL FirstGlance]. <br>		<table><tr><td colspan='2'>[[3zhl]] is a 1 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=3ZHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhd\|3zhd]], [[3zhk\|3zhk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhd\|3zhd]], [[3zhk\|3zhk]]</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=3zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhl RCSB], [http://www.ebi.ac.uk/pdbsum/3zhl 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=3zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhl RCSB], [http://www.ebi.ac.uk/pdbsum/3zhl 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 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Lim, H K.]]	+	[[Category: Lim, H K]]
-	[[Category: Song, H N.]]	+	[[Category: Song, H N]]
-	[[Category: Woo, E J.]]	+	[[Category: Woo, E J]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Single domain antibody]]		[[Category: Single domain antibody]]

OCA at 09:18, 16 July 2014

OCA — Wed, 16 Jul 2014 09:18:32 GMT

←Older revision		Revision as of 09:18, 16 July 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3zhl\| PDB=3zhl \| SCENE= }}~~	+	==The crystal structure of single domain antibody 8-14 scaffold==
-	===The crystal structure of single domain antibody 8-14 scaffold===	+	<StructureSection load='3zhl' size='340' side='right' caption='[[3zhl]], [[Resolution\|resolution]] 2.47Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3zhl]] is a 1 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=3ZHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhd\|3zhd]], [[3zhk\|3zhk]]</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=3zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhl RCSB], [http://www.ebi.ac.uk/pdbsum/3zhl PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.

-	~~==About this Structure==~~	+	Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter.,Kim DS, Song HN, Nam HJ, Kim SG, Park YS, Park JC, Woo EJ, Lim HK PLoS One. 2014 Jun 3;9(6):e98178. doi: 10.1371/journal.pone.0098178. eCollection , 2014. PMID:24892548<ref>PMID:24892548</ref>
-	~~[[3zhl]] is a 1~~ chain ~~structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3ZHL OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
-	[[Category: ~~Bacillus coli migula 1895~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
	[[Category: Lim, H K.]]		[[Category: Lim, H K.]]
	[[Category: Song, H N.]]		[[Category: Song, H N.]]

OCA at 08:27, 16 April 2014

OCA — Wed, 16 Apr 2014 08:27:08 GMT

←Older revision		Revision as of 08:27, 16 April 2014
Line 3:		Line 3:

	==About this Structure==		==About this Structure==
-	[[3zhl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHL OCA].	+	[[3zhl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHL OCA].
		+
		+	==See Also==
		+	*[[Antibody\|Antibody]]
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Lim, H K.]]		[[Category: Lim, H K.]]
	[[Category: Song, H N.]]		[[Category: Song, H N.]]

OCA at 10:35, 8 January 2014

OCA — Wed, 08 Jan 2014 10:35:24 GMT

←Older revision		Revision as of 10:35, 8 January 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3zhl\| PDB=3zhl \| SCENE= }}
		+	===The crystal structure of single domain antibody 8-14 scaffold===

-	~~The entry~~ 3zhl is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3zhl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHL OCA].
-	~~Authors~~: Song, H.-N., Woo, E.-J.~~, Lim, H.-K.~~	+	[[Category: Lim, H K.]]
-		+	[[Category: Song, H N.]]
-	~~Description~~: ~~The crystal structure of single~~ domain antibody ~~8-14 scaffold~~	+	[[Category: Woo, E J.]]
		+	[[Category: Immune system]]
		+	[[Category: Single domain antibody]]

OCA at 12:48, 3 July 2013

OCA — Wed, 03 Jul 2013 12:48:54 GMT

←Older revision		Revision as of 12:48, 3 July 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Song, H.-N., Woo, E.-J., Lim, H.-K.		Authors: Song, H.-N., Woo, E.-J., Lim, H.-K.

	Description: The crystal structure of single domain antibody 8-14 scaffold		Description: The crystal structure of single domain antibody 8-14 scaffold

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

OCA — Wed, 02 Jan 2013 08:40:36 GMT

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

←Older revision

Revision as of 08:40, 2 January 2013

OCA: New page: '''Unreleased structure''' The entry 3zhl is ON HOLD Authors: Song, H.-N., Woo, E.-J., Lim, H.-K. Description: The crystal structure of single domain antibody 8-14 scaffold

OCA — Wed, 02 Jan 2013 08:40:35 GMT

New page: '''Unreleased structure''' The entry 3zhl is ON HOLD Authors: Song, H.-N., Woo, E.-J., Lim, H.-K. Description: The crystal structure of single domain antibody 8-14 scaffold

New page

'''Unreleased structure'''

The entry 3zhl is ON HOLD

Authors: Song, H.-N., Woo, E.-J., Lim, H.-K.

Description: The crystal structure of single domain antibody 8-14 scaffold