4k23 - Revision history

OCA at 14:27, 8 November 2023

OCA — Wed, 08 Nov 2023 14:27:05 GMT

←Older revision		Revision as of 14:27, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K23 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K23 FirstGlance]. <br>
-	</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=4k23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k23 OCA], [https://pdbe.org/4k23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k23 RCSB], [https://www.ebi.ac.uk/pdbsum/4k23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k23 ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4k23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k23 OCA], [https://pdbe.org/4k23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k23 RCSB], [https://www.ebi.ac.uk/pdbsum/4k23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k23 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:37, 30 November 2022

OCA — Wed, 30 Nov 2022 11:37:01 GMT

←Older revision		Revision as of 11:37, 30 November 2022
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	<StructureSection load='4k23' size='340' side='right'caption='[[4k23]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4k23' size='340' side='right'caption='[[4k23]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4K23 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K23 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4k24\|4k24]]</td></tr>~~	+	</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=4k23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k23 OCA], [https://pdbe.org/4k23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k23 RCSB], [https://www.ebi.ac.uk/pdbsum/4k23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k23 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=4k23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k23 OCA], [~~http~~://pdbe.org/4k23 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4k23 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4k23 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4k23 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]]
		+	*[[Sandbox 20009\|Sandbox 20009]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Chen, L]]	+	[[Category: Chen L]]
-	[[Category: Huang, M]]	+	[[Category: Huang M]]
-	[[Category: Yuan, C]]	+	[[Category: Yuan C]]
-	~~[[Category: Immune system~~]]	+

OCA at 04:55, 13 February 2020

OCA — Thu, 13 Feb 2020 04:55:23 GMT

←Older revision		Revision as of 04:55, 13 February 2020
Line 1:		Line 1:

	==Structure of anti-uPAR Fab ATN-658==		==Structure of anti-uPAR Fab ATN-658==
-	<StructureSection load='4k23' size='340' side='right' caption='[[4k23]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4k23' size='340' side='right'caption='[[4k23]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K23 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K23 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 4k23" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4k23" 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: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Chen, L]]		[[Category: Chen, L]]

OCA at 09:50, 11 August 2016

OCA — Thu, 11 Aug 2016 09:50:43 GMT

←Older revision		Revision as of 09:50, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of anti-uPAR Fab ATN-658==		==Structure of anti-uPAR Fab ATN-658==
	<StructureSection load='4k23' size='340' side='right' caption='[[4k23]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4k23' size='340' side='right' caption='[[4k23]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K23 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K23 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4k24\|4k24]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4k24\|4k24]]</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=4k23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k23 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k23 RCSB], [http://www.ebi.ac.uk/pdbsum/4k23 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=4k23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k23 OCA], [http://pdbe.org/4k23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k23 RCSB], [http://www.ebi.ac.uk/pdbsum/4k23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k23 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4k23" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:32, 4 January 2015

OCA — Sun, 04 Jan 2015 13:32:45 GMT

←Older revision		Revision as of 13:32, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4k23~~\| ~~PDB~~=4k23 \| ~~SCENE~~= }}	+	==Structure of anti-uPAR Fab ATN-658==
-	===~~Structure~~ of anti-uPAR Fab ATN-658~~===~~	+	<StructureSection load='4k23' size='340' side='right' caption='[[4k23]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24465541}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4k23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K23 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4k24\|4k24]]</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=4k23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k23 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k23 RCSB], [http://www.ebi.ac.uk/pdbsum/4k23 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The urokinase plasminogen activator receptor (uPAR) plays a role in tumor progression and has been proposed as a target for the treatment of cancer. We recently described the development of a novel humanized monoclonal antibody that targets uPAR and has anti-tumor activity in multiple xenograft animal tumor models. This antibody, ATN-658, does not inhibit ligand binding (i.e. uPA and vitronectin) to uPAR and its mechanism of action remains unclear. As a first step in understanding the anti-tumor activity of ATN-658, we set out to identify the epitope on uPAR to which ATN-658 binds. Guided by comparisons between primate and human uPAR, epitope mapping studies were performed using several orthogonal techniques. Systematic site directed and alanine scanning mutagenesis identified the region of aa 268-275 of uPAR as the epitope for ATN-658. No known function has previously been attributed to this epitope Structural insights into epitope recognition were obtained from structural studies of the Fab fragment of ATN-658 bound to uPAR. The structure shows that the ATN-658 binds to the DIII domain of uPAR, close to the C-terminus of the receptor, corroborating the epitope mapping results. Intriguingly, when bound to uPAR, the complementarity determining region (CDR) regions of ATN-658 closely mimic the binding regions of the integrin CD11b (alphaM), a previously identified uPAR ligand thought to be involved in leukocyte rolling, migration and complement fixation with no known role in tumor progression of solid tumors. These studies reveal a new functional epitope on uPAR involved in tumor progression and demonstrate a previously unrecognized strategy for the therapeutic targeting of uPAR.

-	~~==About this Structure==~~	+	Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b (alphaM).,Xu X, Cai Y, Wei Y, Donate F, Juarez J, Parry G, Chen L, Meehan EJ, Ahn RW, Ugolkov A, Dubrovskyi O, O'Halloran TV, Huang M, Mazar AP PLoS One. 2014 Jan 21;9(1):e85349. doi: 10.1371/journal.pone.0085349. eCollection, 2014 Jan 21. PMID:24465541<ref>PMID:24465541</ref>
-	~~[[4k23]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4K23 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024465541</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Chen, L.]]	+	[[Category: Chen, L]]
-	[[Category: Huang, M.]]	+	[[Category: Huang, M]]
-	[[Category: Yuan, C.]]	+	[[Category: Yuan, C]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 17:51, 3 March 2014

OCA — Mon, 03 Mar 2014 17:51:56 GMT

←Older revision		Revision as of 17:51, 3 March 2014
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4k23\| PDB=4k23 \| SCENE= }}
		+	===Structure of anti-uPAR Fab ATN-658===
		+	{{ABSTRACT_PUBMED_24465541}}

-	~~The entry~~ 4k23 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4k23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K23 OCA].

-	~~Authors~~: ~~Yuan~~, C., Huang, M., ~~Chen, L~~.	+	==Reference==
-		+	<ref group="xtra">PMID:024465541</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Structure of anti-uPAR Fab ATN-658~~	+	[[Category: Mus musculus]]
		+	[[Category: Chen, L.]]
		+	[[Category: Huang, M.]]
		+	[[Category: Yuan, C.]]
		+	[[Category: Immune system]]

OCA at 11:25, 19 June 2013

OCA — Wed, 19 Jun 2013 11:25:55 GMT

←Older revision		Revision as of 11:25, 19 June 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4k23 is ON HOLD	+	The entry 4k23 is ON HOLD until Paper Publication

	Authors: Yuan, C., Huang, M., Chen, L.		Authors: Yuan, C., Huang, M., Chen, L.

	Description: Structure of anti-uPAR Fab ATN-658		Description: Structure of anti-uPAR Fab ATN-658

OCA: Protected "4k23" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2013 20:06:23 GMT

Protected "4k23" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:06, 17 April 2013

OCA: New page: '''Unreleased structure''' The entry 4k23 is ON HOLD Authors: Yuan, C., Huang, M., Chen, L. Description: Structure of anti-uPAR Fab ATN-658

OCA — Wed, 17 Apr 2013 20:06:22 GMT

New page: '''Unreleased structure''' The entry 4k23 is ON HOLD Authors: Yuan, C., Huang, M., Chen, L. Description: Structure of anti-uPAR Fab ATN-658

New page

'''Unreleased structure'''

The entry 4k23 is ON HOLD

Authors: Yuan, C., Huang, M., Chen, L.

Description: Structure of anti-uPAR Fab ATN-658