6df2 - Revision history

OCA at 06:05, 11 October 2023

2023-10-11T06:05:10Z

← Older revision		Revision as of 06:05, 11 October 2023
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	<StructureSection load='6df2' size='340' side='right'caption='[[6df2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6df2' size='340' side='right'caption='[[6df2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6df2]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DF2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DF2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6df2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DF2 FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</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]] 2.6Å</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=6df2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6df2 OCA], [~~http~~://pdbe.org/6df2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6df2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6df2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6df2 ProSAT]</span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</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=6df2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6df2 OCA], [https://pdbe.org/6df2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6df2 RCSB], [https://www.ebi.ac.uk/pdbsum/6df2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6df2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
			*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Synthetic construct ~~sequences~~]]		[[Category: Synthetic construct]]
	[[Category: Leung, K]]		[[Category: Leung K]]
	[[Category: Mou, K]]		[[Category: Mou K]]
	[[Category: Wells~~, J A]]~~		[[Category: Wells JA]]
	~~[[Category: Antibody]]~~
	~~[[Category: Immune system]]~~
	~~[[Category: Recombination~~]]

OCA at 09:08, 1 May 2019

2019-05-01T09:08:32Z

← Older revision		Revision as of 09:08, 1 May 2019
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	==Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine peptide==		==Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine peptide==
	<StructureSection load='6df2' size='340' side='right' caption='[[6df2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6df2' size='340' side='right'caption='[[6df2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6df2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DF2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6df2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DF2 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6df2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6df2" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Leung, K]]		[[Category: Leung, K]]

OCA at 20:27, 2 December 2018

2018-12-02T20:27:18Z

← Older revision		Revision as of 20:27, 2 December 2018
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6df2 is ~~ON HOLD until Paper~~ Publication		==Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine peptide==
			<StructureSection load='6df2' size='340' side='right' caption='[[6df2]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6df2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DF2 FirstGlance]. <br>
			</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></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=6df2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6df2 OCA], [http://pdbe.org/6df2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6df2 RCSB], [http://www.ebi.ac.uk/pdbsum/6df2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6df2 ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Phosphotyrosine (pY) is one of the most highly studied posttranslational modifications that is responsible for tightly regulating many signaling pathways in eukaryotes. Pan-specific pY antibodies have emerged as powerful tools for understanding the role of these modifications. Nevertheless, structures have not been reported for pan-specific pY antibodies, greatly impeding the further development of tools for integrating this ubiquitous posttranslational modification using structure-guided designs. Here, we present the first crystal structures of two widely utilized pan-specific pY antibodies, PY20 and 4G10. The two antibodies, although developed independently from animal immunizations, have surprisingly similar modes of recognition of the phosphate group, implicating a generic binding structure among pan-specific pY antibodies. Sequence alignments revealed that many pY binding residues are predominant in the mouse V germline genes, which consequently led to the convergent antibodies. On the basis of the convergent structure, we designed a phage display library by lengthening the CDR-L3 loop with the aid of computational modeling. Panning with this library resulted in a series of 4G10 variants with 4 to 11-fold improvements in pY binding affinities. The crystal structure of one improved variant showed remarkable superposition to the computational model, where the lengthened CDR-L3 loop creates an additional hydrogen bond indirectly bound to the phosphate group via a water molecule. The engineered variants exhibited superior performance in Western blot and immunofluorescence.

	~~Authors:~~ Mou, K., ~~Leung~~, K., Wells, J.A.		Engineering Improved Antiphosphotyrosine Antibodies Based on an Immunoconvergent Binding Motif.,Mou Y, Zhou XX, Leung K, Martinko AJ, Yu JY, Chen W, Wells JA J Am Chem Soc. 2018 Nov 19. doi: 10.1021/jacs.8b08402. PMID:30398859<ref>PMID:30398859</ref>

	~~Description: Improved anti~~-~~phosphotyrosine antibody 4G10~~-~~S5-4D5 Fab complexed with phosphotyrosine peptide~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
			<div class="pdbe-citations 6df2" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Synthetic construct sequences]]
			[[Category: Leung, K]]
	[[Category: Mou, K]]		[[Category: Mou, K]]
	[[Category: Wells, J.A]]		[[Category: Wells, J A]]
	[[Category: ~~Leung, K~~]]		[[Category: Antibody]]
			[[Category: Immune system]]
			[[Category: Recombination]]

OCA at 04:16, 6 June 2018

2018-06-06T04:16:58Z

← Older revision		Revision as of 04:16, 6 June 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6df2 is ON HOLD		The entry 6df2 is ON HOLD until Paper Publication

	Authors: Mou, K., Leung, K., Wells, J.A.		Authors: Mou, K., Leung, K., Wells, J.A.

OCA at 04:04, 30 May 2018

2018-05-30T04:04:30Z

← Older revision		Revision as of 04:04, 30 May 2018
Line 5:		Line 5:
	Authors: Mou, K., Leung, K., Wells, J.A.		Authors: Mou, K., Leung, K., Wells, J.A.

	Description: anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with ~~sulfate~~		Description: Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine peptide
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Mou, K]]		[[Category: Mou, K]]
	[[Category: Wells, J.A]]		[[Category: Wells, J.A]]
	[[Category: Leung, K]]		[[Category: Leung, K]]

OCA: Protected "6df2" [edit=sysop:move=sysop]

2018-05-23T06:01:48Z

Protected "6df2" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:01, 23 May 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6df2 is ON HOLD Authors: Mou, K., Leung, K., Wells, J.A. Description: anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with sulfate [[Category:...

2018-05-23T06:01:47Z

New page: '''Unreleased structure''' The entry 6df2 is ON HOLD Authors: Mou, K., Leung, K., Wells, J.A. Description: anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with sulfate [[Category:...

New page

'''Unreleased structure'''

The entry 6df2 is ON HOLD

Authors: Mou, K., Leung, K., Wells, J.A.

Description: anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with sulfate
[[Category: Unreleased Structures]]
[[Category: Mou, K]]
[[Category: Wells, J.A]]
[[Category: Leung, K]]