6jbt - Revision history

OCA at 10:06, 22 November 2023

OCA — Wed, 22 Nov 2023 10:06:13 GMT

←Older revision		Revision as of 10:06, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6jbt' size='340' side='right'caption='[[6jbt]], [[Resolution\|resolution]] 2.47Å' scene=''>		<StructureSection load='6jbt' size='340' side='right'caption='[[6jbt]], [[Resolution\|resolution]] 2.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jbt]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JBT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jbt]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JBT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=FUC:ALPHA~~-~~L-FUCOSE'>FUC</scene>~~, ~~<scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.47Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PDCD1, PD1 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6jbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbt OCA], [~~http~~://pdbe.org/6jbt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jbt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jbt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbt 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=6jbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbt OCA], [https://pdbe.org/6jbt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jbt RCSB], [https://www.ebi.ac.uk/pdbsum/6jbt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbt ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Systemic lupus erythematosus;Multiple sclerosis. Systemic lupus erythematosus 2 (SLEB2) [MIM:[~~http~~://omim.org/entry/605218 605218]]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.<ref>PMID:12402038</ref>	+	[https://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN] Systemic lupus erythematosus;Multiple sclerosis. Systemic lupus erythematosus 2 (SLEB2) [MIM:[https://omim.org/entry/605218 605218]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.<ref>PMID:12402038</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.<ref>PMID:21276005</ref>	+	[https://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN] Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.<ref>PMID:21276005</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6jbt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jbt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cell death protein 3D structures\|Cell death protein 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Chai, Y]]	+	[[Category: Chai Y]]
-	[[Category: Gao~~, G F~~]]	+	[[Category: Gao GF]]
-	[[Category: Guo, L]]	+	[[Category: Guo L]]
-	[[Category: Qi, J]]	+	[[Category: Qi J]]
-	[[Category: Tan, S]]	+	[[Category: Tan S]]
-	[[Category: Yan, J]]	+	[[Category: Yan J]]
-	~~[[Category: Complex structure]]~~	+
-	~~[[Category: Glycosylation]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Pd-1]]~~	+
-	~~[[Category: Toripalimab-fab~~]]	+

OCA at 12:57, 25 December 2019

OCA — Wed, 25 Dec 2019 12:57:19 GMT

←Older revision		Revision as of 12:57, 25 December 2019
Line 3:		Line 3:
	<StructureSection load='6jbt' size='340' side='right'caption='[[6jbt]], [[Resolution\|resolution]] 2.47Å' scene=''>		<StructureSection load='6jbt' size='340' side='right'caption='[[6jbt]], [[Resolution\|resolution]] 2.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jbt]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jbt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDCD1, PD1 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6jbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbt OCA], [http://pdbe.org/6jbt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbt RCSB], [http://www.ebi.ac.uk/pdbsum/6jbt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbt 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=6jbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbt OCA], [http://pdbe.org/6jbt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbt RCSB], [http://www.ebi.ac.uk/pdbsum/6jbt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbt ProSAT]</span></td></tr>
	</table>		</table>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Chai, Y]]		[[Category: Chai, Y]]
	[[Category: Gao, G F]]		[[Category: Gao, G F]]

OCA at 05:56, 19 June 2019

OCA — Wed, 19 Jun 2019 05:56:53 GMT

←Older revision		Revision as of 05:56, 19 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jbt is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Complex structure of toripalimab-Fab and PD-1==
		+	<StructureSection load='6jbt' size='340' side='right'caption='[[6jbt]], [[Resolution\|resolution]] 2.47Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jbt]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6jbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbt OCA], [http://pdbe.org/6jbt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbt RCSB], [http://www.ebi.ac.uk/pdbsum/6jbt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbt ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Systemic lupus erythematosus;Multiple sclerosis. Systemic lupus erythematosus 2 (SLEB2) [MIM:[http://omim.org/entry/605218 605218]]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.<ref>PMID:12402038</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDCD1_HUMAN PDCD1_HUMAN]] Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.<ref>PMID:21276005</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Monoclonal antibody (mAb)-based blockade of programmed cell death 1 (PD-1) or its ligand to enable antitumor T-cell immunity has been successful in treating multiple tumors. However, the structural basis of the binding mechanisms of the mAbs and PD-1 and the effects of glycosylation of PD-1 on mAb interaction are not well understood. Here, we report the complex structure of PD-1 with toripalimab, a mAb that is approved by China National Medical Products Administration as a second-line treatment for melanoma and is under multiple Phase 1-Phase 3 clinical trials in both China and the US. Our analysis reveals that toripalimab mainly binds to the FG loop of PD-1 with an unconventionally long complementarity-determining region 3 loop of the heavy chain, which is distinct from the known binding epitopes of anti-PD-1 mAbs with structural evidences. The glycan modifications of PD-1 could be observed in three potential N-linked glycosylation sites, while no substantial influences were detected to the binding of toripalimab. These findings benefit our understanding of the binding mechanisms of toripalimab to PD-1 and shed light for future development of biologics targeting PD-1. Atomic coordinates have been deposited in the Protein Data Bank under accession code 6JBT.

-	~~Authors~~:	+	Glycosylation-independent binding of monoclonal antibody toripalimab to FG loop of PD-1 for tumor immune checkpoint therapy.,Liu H, Guo L, Zhang J, Zhou Y, Zhou J, Yao J, Wu H, Yao S, Chen B, Chai Y, Qi J, Gao GF, Tan S, Feng H, Yan J MAbs. 2019 May/Jun;11(4):681-690. doi: 10.1080/19420862.2019.1596513. Epub 2019, Apr 19. PMID:30892132<ref>PMID:30892132</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6jbt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chai, Y]]
		+	[[Category: Gao, G F]]
		+	[[Category: Guo, L]]
		+	[[Category: Qi, J]]
		+	[[Category: Tan, S]]
		+	[[Category: Yan, J]]
		+	[[Category: Complex structure]]
		+	[[Category: Glycosylation]]
		+	[[Category: Immune system]]
		+	[[Category: Pd-1]]
		+	[[Category: Toripalimab-fab]]

OCA at 09:59, 13 March 2019

OCA — Wed, 13 Mar 2019 09:59:07 GMT

←Older revision		Revision as of 09:59, 13 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jbt is ON HOLD	+	The entry 6jbt is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 13 Feb 2019 07:19:45 GMT

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

←Older revision

Revision as of 07:19, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6jbt is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Feb 2019 07:19:43 GMT

New page: '''Unreleased structure''' The entry 6jbt is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6jbt is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]