6umv - Revision history

OCA at 07:54, 11 October 2023

OCA — Wed, 11 Oct 2023 07:54:36 GMT

←Older revision		Revision as of 07:54, 11 October 2023
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	<StructureSection load='6umv' size='340' side='right'caption='[[6umv]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='6umv' size='340' side='right'caption='[[6umv]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6umv]] 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=6UMV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6umv]] is a 1 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=6UMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UMV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.424Å</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=CL:CHLORIDE+ION'>CL</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=6umv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6umv OCA], [~~http~~://pdbe.org/6umv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6umv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6umv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6umv 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=6umv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6umv OCA], [https://pdbe.org/6umv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6umv RCSB], [https://www.ebi.ac.uk/pdbsum/6umv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6umv 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 ==
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	</div>		</div>
	<div class="pdbe-citations 6umv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6umv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cell death protein 3D structures\|Cell death protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, P S~~]]	+	[[Category: Kim PS]]
-	[[Category: Tang, S]]	+	[[Category: Tang S]]
-	~~[[Category: Immune checkpoint]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Pd-1~~]]	+

OCA at 13:23, 18 December 2019

OCA — Wed, 18 Dec 2019 13:23:41 GMT

←Older revision		Revision as of 13:23, 18 December 2019
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	<StructureSection load='6umv' size='340' side='right'caption='[[6umv]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='6umv' size='340' side='right'caption='[[6umv]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6umv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6umv]] 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=6UMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UMV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=6umv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6umv OCA], [http://pdbe.org/6umv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6umv RCSB], [http://www.ebi.ac.uk/pdbsum/6umv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6umv 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=6umv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6umv OCA], [http://pdbe.org/6umv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6umv RCSB], [http://www.ebi.ac.uk/pdbsum/6umv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6umv ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kim, P S]]		[[Category: Kim, P S]]

OCA at 07:02, 27 November 2019

OCA — Wed, 27 Nov 2019 07:02:34 GMT

←Older revision		Revision as of 07:02, 27 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6umv is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Human apo PD-1 double mutant==
		+	<StructureSection load='6umv' size='340' side='right'caption='[[6umv]], [[Resolution\|resolution]] 1.42Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6umv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UMV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=6umv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6umv OCA], [http://pdbe.org/6umv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6umv RCSB], [http://www.ebi.ac.uk/pdbsum/6umv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6umv 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 ==
		+	Immune checkpoint blockade of programmed death-1 (PD-1) by monoclonal antibody drugs has delivered breakthroughs in the treatment of cancer. Nonetheless, small-molecule PD-1 inhibitors could lead to increases in treatment efficacy, safety, and global access. While the ligand-binding surface of apo-PD-1 is relatively flat, it harbors a striking pocket in the murine PD-1/PD-L2 structure. An analogous pocket in human PD-1 may serve as a small-molecule drug target, but the structure of the human complex is unknown. Because the CC' and FG loops in murine PD-1 adopt new conformations upon binding PD-L2, we hypothesized that mutations in these two loops could be coupled to pocket formation and alter PD-1's affinity for PD-L2. Here, we conducted deep mutational scanning in these loops and used yeast surface display to select for enhanced PD-L2 binding. A PD-1 variant with three substitutions binds PD-L2 with an affinity two orders of magnitude higher than that of the wild-type protein, permitting crystallization of the complex. We determined the X-ray crystal structures of the human triple-mutant PD-1/PD-L2 complex and the apo triple-mutant PD-1 variant at 2.0 A and 1.2 A resolution, respectively. Binding of PD-L2 is accompanied by formation of a prominent pocket in human PD-1, as well as substantial conformational changes in the CC' and FG loops. The structure of the apo triple-mutant PD-1 shows that the CC' loop adopts the ligand-bound conformation, providing support for allostery between the loop and pocket. This human PD-1/PD-L2 structure provide critical insights for the design and discovery of small-molecule PD-1 inhibitors.

-	~~Authors~~:	+	A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.,Tang S, Kim PS Proc Natl Acad Sci U S A. 2019 Nov 14. pii: 1916916116. doi:, 10.1073/pnas.1916916116. PMID:31727844<ref>PMID:31727844</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6umv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kim, P S]]
		+	[[Category: Tang, S]]
		+	[[Category: Immune checkpoint]]
		+	[[Category: Immune system]]
		+	[[Category: Pd-1]]

OCA at 05:17, 6 November 2019

OCA — Wed, 06 Nov 2019 05:17:17 GMT

←Older revision		Revision as of 05:17, 6 November 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 16 Oct 2019 04:42:44 GMT

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

←Older revision

Revision as of 04:42, 16 October 2019

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

OCA — Wed, 16 Oct 2019 04:42:43 GMT

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

New page

'''Unreleased structure'''

The entry 6umv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]