5dmj - Revision history

OCA at 21:50, 28 June 2023

OCA — Wed, 28 Jun 2023 21:50:04 GMT

←Older revision		Revision as of 21:50, 28 June 2023
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	<StructureSection load='5dmj' size='340' side='right'caption='[[5dmj]], [[Resolution\|resolution]] 2.79Å' scene=''>		<StructureSection load='5dmj' size='340' side='right'caption='[[5dmj]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dmj]] is a 6 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=5DMJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DMJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dmj]] is a 6 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=5DMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DMJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.79Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5dmi\|5dmi]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CD40, TNFRSF5 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmj OCA], [https://pdbe.org/5dmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dmj RCSB], [https://www.ebi.ac.uk/pdbsum/5dmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmj ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmj OCA], [~~http~~://pdbe.org/5dmj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dmj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dmj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN]] Defects in CD40 are the cause of immunodeficiency with hyper-IgM type 3 (HIGM3) [MIM:[~~http~~://omim.org/entry/606843 606843]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:11675497</ref>	+	[https://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN] Defects in CD40 are the cause of immunodeficiency with hyper-IgM type 3 (HIGM3) [MIM:[https://omim.org/entry/606843 606843]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:11675497</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN]] Receptor for TNFSF5/CD40LG.	+	[https://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN] Receptor for TNFSF5/CD40LG.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Tumor necrosis factor receptor 3D structures\|Tumor necrosis factor receptor 3D structures]]		*[[Tumor necrosis factor receptor 3D structures\|Tumor necrosis factor receptor 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sheriff, S]]	+	[[Category: Sheriff S]]
-	~~[[Category: Cell surface receptor]]~~	+
-	~~[[Category: Domain antibody]]~~	+
-	~~[[Category: Immune system-signaling protein complex]]~~	+
-	~~[[Category: Protein/protein interaction~~]]	+

OCA at 08:10, 8 April 2020

OCA — Wed, 08 Apr 2020 08:10:20 GMT

←Older revision		Revision as of 08:10, 8 April 2020
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	==Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB==		==Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB==
-	<StructureSection load='5dmj' size='340' side='right' caption='[[5dmj]], [[Resolution\|resolution]] 2.79Å' scene=''>	+	<StructureSection load='5dmj' size='340' side='right'caption='[[5dmj]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dmj]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DMJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dmj]] is a 6 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=5DMJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DMJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dmi\|5dmi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dmi\|5dmi]]</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=5dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmj OCA], [http://pdbe.org/5dmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmj RCSB], [http://www.ebi.ac.uk/pdbsum/5dmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmj ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD40, TNFRSF5 ([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://proteopedia.org/fgij/fg.htm?mol=5dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmj OCA], [http://pdbe.org/5dmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmj RCSB], [http://www.ebi.ac.uk/pdbsum/5dmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmj ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	</div>		</div>
	<div class="pdbe-citations 5dmj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dmj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Tumor necrosis factor receptor 3D structures\|Tumor necrosis factor receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Sheriff, S]]		[[Category: Sheriff, S]]
	[[Category: Cell surface receptor]]		[[Category: Cell surface receptor]]

OCA at 06:25, 26 July 2016

OCA — Tue, 26 Jul 2016 06:25:46 GMT

←Older revision		Revision as of 06:25, 26 July 2016
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dmi\|5dmi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dmi\|5dmi]]</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=5dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmj OCA], [http://pdbe.org/5dmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmj RCSB], [http://www.ebi.ac.uk/pdbsum/5dmj 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=5dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmj OCA], [http://pdbe.org/5dmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmj RCSB], [http://www.ebi.ac.uk/pdbsum/5dmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmj ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 07:36, 20 June 2016

OCA — Mon, 20 Jun 2016 07:36:37 GMT

←Older revision		Revision as of 07:36, 20 June 2016
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN]] Receptor for TNFSF5/CD40LG.		[[http://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN]] Receptor for TNFSF5/CD40LG.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Current clinical anti-CD40 biologic agents include both antagonist molecules for the treatment of autoimmune diseases, and agonist molecules for immuno-oncology, yet the relationship between CD40 epitope and these opposing biological outcomes is not well defined. This report describes the identification of potent antagonist domain antibodies (dAbs) that bind to a novel human-CD40 specific epitope which is divergent in the CD40 of non-human primates. A similarly selected anti-cynomolgus-CD40 dAb recognizing the homologous epitope is also a potent antagonist. Mutagenesis, biochemical, and X-ray crystallography studies demonstrate that the epitope is distinct from that of CD40 agonists. Both the human-specific and cynomolgus-specific molecules remain pure antagonists even when formatted as bivalent Fc-fusion proteins, making this an attractive therapeutic format for targeting hCD40 in autoimmune indications.
		+
		+	Functional antagonism of human CD40 achieved by targeting a unique species-specific epitope.,Yamniuk AP, Suri A, Krystek SR, Tamura J, Ramamurthy V, Kuhn R, Carroll K, Fleener C, Ryseck R, Cheng L, An Y, Drew P, Grant S, Suchard SJ, Nadler SG, Bryson JW, Sheriff S J Mol Biol. 2016 May 21. pii: S0022-2836(16)30169-3. doi:, 10.1016/j.jmb.2016.05.014. PMID:27216500<ref>PMID:27216500</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dmj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:06, 2 June 2016

OCA — Thu, 02 Jun 2016 06:06:50 GMT

←Older revision		Revision as of 06:06, 2 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5dmj is ON HOLD until Paper Publication~~	+	==Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB==
-		+	<StructureSection load='5dmj' size='340' side='right' caption='[[5dmj]], [[Resolution\|resolution]] 2.79Å' scene=''>
-	~~Authors: Sheriff, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dmj]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DMJ FirstGlance]. <br>
-	~~Description:~~ Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dmi\|5dmi]]</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=5dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmj OCA], [http://pdbe.org/5dmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmj RCSB], [http://www.ebi.ac.uk/pdbsum/5dmj PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN]] Defects in CD40 are the cause of immunodeficiency with hyper-IgM type 3 (HIGM3) [MIM:[http://omim.org/entry/606843 606843]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:11675497</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TNR5_HUMAN TNR5_HUMAN]] Receptor for TNFSF5/CD40LG.
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Sheriff, S]]		[[Category: Sheriff, S]]
		+	[[Category: Cell surface receptor]]
		+	[[Category: Domain antibody]]
		+	[[Category: Immune system-signaling protein complex]]
		+	[[Category: Protein/protein interaction]]

OCA at 02:29, 16 October 2015

OCA — Fri, 16 Oct 2015 02:29:25 GMT

←Older revision		Revision as of 02:29, 16 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5dmj is ON HOLD	+	The entry 5dmj is ON HOLD until Paper Publication

	Authors: Sheriff, S.		Authors: Sheriff, S.

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

OCA — Wed, 30 Sep 2015 13:10:23 GMT

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

←Older revision

Revision as of 13:10, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dmj is ON HOLD Authors: Sheriff, S. Description: Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB [[Category: Unreleas...

OCA — Wed, 30 Sep 2015 13:10:22 GMT

New page: '''Unreleased structure''' The entry 5dmj is ON HOLD Authors: Sheriff, S. Description: Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5dmj is ON HOLD

Authors: Sheriff, S.

Description: Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB
[[Category: Unreleased Structures]]
[[Category: Sheriff, S]]