7r84 - Revision history

OCA at 07:19, 3 April 2024

OCA — Wed, 03 Apr 2024 07:19:40 GMT

←Older revision		Revision as of 07:19, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='7r84' size='340' side='right'caption='[[7r84]], [[Resolution\|resolution]] 1.34Å' scene=''>		<StructureSection load='7r84' size='340' side='right'caption='[[7r84]], [[Resolution\|resolution]] 1.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7r84]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7r84]] is a 4 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=7R84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R84 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=~~MAN~~:ALPHA-D-~~MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~FUC~~:ALPHA-L-~~FUCOSE~~'>~~FUC~~</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]] 1.336Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=7r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r84 OCA], [https://pdbe.org/7r84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r84 RCSB], [https://www.ebi.ac.uk/pdbsum/7r84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r84 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=7r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r84 OCA], [https://pdbe.org/7r84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r84 RCSB], [https://www.ebi.ac.uk/pdbsum/7r84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r84 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AGRB1_MOUSE AGRB1_MOUSE]] Phosphatidylserine receptor which enhances the engulfment of apoptotic cells (PubMed:17960134). Also mediates the binding and engulfment of Gram-negative bacteria (PubMed:21245295, PubMed:26838550, PubMed:26838550). Stimulates production of reactive oxygen species by macrophages in response to Gram-negative bacteria, resulting in enhanced microbicidal macrophage activity (By similarity). In the gastric mucosa, required for recognition and engulfment of apoptotic gastric epithelial cells (By similarity). Promotes myoblast fusion (PubMed:23615608). Activates the Rho pathway in a G-protein-dependent manner (By similarity). Inhibits MDM2-mediated ubiquitination and degradation of DLG4/PSD95, promoting DLG4 stability and regulating synaptic plasticity (PubMed:25751059). Required for the formation of dendritic spines by ensuring the correct localization of PARD3 and TIAM1 (By similarity). Potent inhibitor of angiogenesis in brain and may play a significant role as a mediator of the p53/TP53 signal in suppression of glioblastoma (By similarity).[UniProtKB:C0HL12][UniProtKB:O14514]<ref>PMID:11875720</ref> <ref>PMID:17960134</ref> <ref>PMID:21245295</ref> <ref>PMID:23615608</ref> <ref>PMID:25751059</ref> <ref>PMID:26838550</ref> Inhibits angiogenesis in a CD36-dependent manner.[UniProtKB:O14514] Inhibits angiogenesis.[UniProtKB:O14514]	+	[https://www.uniprot.org/uniprot/AGRB1_MOUSE AGRB1_MOUSE] Phosphatidylserine receptor which enhances the engulfment of apoptotic cells (PubMed:17960134). Also mediates the binding and engulfment of Gram-negative bacteria (PubMed:21245295, PubMed:26838550, PubMed:26838550). Stimulates production of reactive oxygen species by macrophages in response to Gram-negative bacteria, resulting in enhanced microbicidal macrophage activity (By similarity). In the gastric mucosa, required for recognition and engulfment of apoptotic gastric epithelial cells (By similarity). Promotes myoblast fusion (PubMed:23615608). Activates the Rho pathway in a G-protein-dependent manner (By similarity). Inhibits MDM2-mediated ubiquitination and degradation of DLG4/PSD95, promoting DLG4 stability and regulating synaptic plasticity (PubMed:25751059). Required for the formation of dendritic spines by ensuring the correct localization of PARD3 and TIAM1 (By similarity). Potent inhibitor of angiogenesis in brain and may play a significant role as a mediator of the p53/TP53 signal in suppression of glioblastoma (By similarity).[UniProtKB:C0HL12][UniProtKB:O14514]<ref>PMID:11875720</ref> <ref>PMID:17960134</ref> <ref>PMID:21245295</ref> <ref>PMID:23615608</ref> <ref>PMID:25751059</ref> <ref>PMID:26838550</ref> Inhibits angiogenesis in a CD36-dependent manner.[UniProtKB:O14514] Inhibits angiogenesis.[UniProtKB:O14514]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	RTN4-binding proteins were widely studied as "NoGo" receptors, but their physiological interactors and roles remain elusive. Similarly, BAI adhesion-GPCRs were associated with numerous activities, but their ligands and functions remain unclear. Using unbiased approaches, we observed an unexpected convergence: RTN4 receptors are high-affinity ligands for BAI adhesion-GPCRs. A single thrombospondin type 1-repeat (TSR) domain of BAIs binds to the leucine-rich repeat domain of all three RTN4-receptor isoforms with nanomolar affinity. In the 1.65 A crystal structure of the BAI1/RTN4-receptor complex, C-mannosylation of tryptophan and O-fucosylation of threonine in the BAI TSR-domains creates a RTN4-receptor/BAI interface shaped by unusual glycoconjugates that enables high-affinity interactions. In human neurons, RTN4 receptors regulate dendritic arborization, axonal elongation, and synapse formation by differential binding to glial versus neuronal BAIs, thereby controlling neural network activity. Thus, BAI binding to RTN4/NoGo receptors represents a receptor-ligand axis that, enabled by rare post-translational modifications, controls development of synaptic circuits.	+
-		+
-	RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development.,Wang J, Miao Y, Wicklein R, Sun Z, Wang J, Jude KM, Fernandes RA, Merrill SA, Wernig M, Garcia KC, Sudhof TC Cell. 2021 Nov 24;184(24):5869-5885.e25. doi: 10.1016/j.cell.2021.10.016. Epub, 2021 Nov 9. PMID:34758294<ref>PMID:34758294</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7r84" style="background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 15:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Garcia, K C~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Jude, K M~~]]	+	[[Category: Garcia KC]]
-	[[Category: ~~Miao, Y~~]]	+	[[Category: Jude KM]]
-	[[Category: ~~Adhesion gpcr]]~~	+	[[Category: Miao Y]]
-	~~[[Category: C-mannosylation]]~~	+
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: O-linked glycosylation~~]]	+

OCA at 08:14, 25 May 2022

OCA — Wed, 25 May 2022 08:14:46 GMT

←Older revision		Revision as of 08:14, 25 May 2022
Line 1:		Line 1:

	==Structure of mouse BAI1 (ADGRB1) TSR3 domain in P21 space group==		==Structure of mouse BAI1 (ADGRB1) TSR3 domain in P21 space group==
-	<StructureSection load='7r84' size='340' side='right'caption='[[7r84]]' scene=''>	+	<StructureSection load='7r84' size='340' side='right'caption='[[7r84]], [[Resolution\|resolution]] 1.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7r84]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R84 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=7r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r84 OCA], [https://pdbe.org/7r84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r84 RCSB], [https://www.ebi.ac.uk/pdbsum/7r84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r84 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</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=7r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r84 OCA], [https://pdbe.org/7r84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r84 RCSB], [https://www.ebi.ac.uk/pdbsum/7r84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r84 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/AGRB1_MOUSE AGRB1_MOUSE]] Phosphatidylserine receptor which enhances the engulfment of apoptotic cells (PubMed:17960134). Also mediates the binding and engulfment of Gram-negative bacteria (PubMed:21245295, PubMed:26838550, PubMed:26838550). Stimulates production of reactive oxygen species by macrophages in response to Gram-negative bacteria, resulting in enhanced microbicidal macrophage activity (By similarity). In the gastric mucosa, required for recognition and engulfment of apoptotic gastric epithelial cells (By similarity). Promotes myoblast fusion (PubMed:23615608). Activates the Rho pathway in a G-protein-dependent manner (By similarity). Inhibits MDM2-mediated ubiquitination and degradation of DLG4/PSD95, promoting DLG4 stability and regulating synaptic plasticity (PubMed:25751059). Required for the formation of dendritic spines by ensuring the correct localization of PARD3 and TIAM1 (By similarity). Potent inhibitor of angiogenesis in brain and may play a significant role as a mediator of the p53/TP53 signal in suppression of glioblastoma (By similarity).[UniProtKB:C0HL12][UniProtKB:O14514]<ref>PMID:11875720</ref> <ref>PMID:17960134</ref> <ref>PMID:21245295</ref> <ref>PMID:23615608</ref> <ref>PMID:25751059</ref> <ref>PMID:26838550</ref> Inhibits angiogenesis in a CD36-dependent manner.[UniProtKB:O14514] Inhibits angiogenesis.[UniProtKB:O14514]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RTN4-binding proteins were widely studied as "NoGo" receptors, but their physiological interactors and roles remain elusive. Similarly, BAI adhesion-GPCRs were associated with numerous activities, but their ligands and functions remain unclear. Using unbiased approaches, we observed an unexpected convergence: RTN4 receptors are high-affinity ligands for BAI adhesion-GPCRs. A single thrombospondin type 1-repeat (TSR) domain of BAIs binds to the leucine-rich repeat domain of all three RTN4-receptor isoforms with nanomolar affinity. In the 1.65 A crystal structure of the BAI1/RTN4-receptor complex, C-mannosylation of tryptophan and O-fucosylation of threonine in the BAI TSR-domains creates a RTN4-receptor/BAI interface shaped by unusual glycoconjugates that enables high-affinity interactions. In human neurons, RTN4 receptors regulate dendritic arborization, axonal elongation, and synapse formation by differential binding to glial versus neuronal BAIs, thereby controlling neural network activity. Thus, BAI binding to RTN4/NoGo receptors represents a receptor-ligand axis that, enabled by rare post-translational modifications, controls development of synaptic circuits.
		+
		+	RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development.,Wang J, Miao Y, Wicklein R, Sun Z, Wang J, Jude KM, Fernandes RA, Merrill SA, Wernig M, Garcia KC, Sudhof TC Cell. 2021 Nov 24;184(24):5869-5885.e25. doi: 10.1016/j.cell.2021.10.016. Epub, 2021 Nov 9. PMID:34758294<ref>PMID:34758294</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7r84" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Garcia KC]]	+	[[Category: Garcia, K C]]
-	[[Category: Jude KM]]	+	[[Category: Jude, K M]]
-	[[Category: Miao Y]]	+	[[Category: Miao, Y]]
		+	[[Category: Adhesion gpcr]]
		+	[[Category: C-mannosylation]]
		+	[[Category: Cell adhesion]]
		+	[[Category: O-linked glycosylation]]

OCA at 06:16, 10 November 2021

OCA — Wed, 10 Nov 2021 06:16:33 GMT

←Older revision		Revision as of 06:16, 10 November 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7r84 is ~~ON HOLD until Paper Publication~~	+	==Structure of mouse BAI1 (ADGRB1) TSR3 domain in P21 space group==
-		+	<StructureSection load='7r84' size='340' side='right'caption='[[7r84]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R84 FirstGlance]. <br>
-	~~Description~~:	+	</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=7r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r84 OCA], [https://pdbe.org/7r84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r84 RCSB], [https://www.ebi.ac.uk/pdbsum/7r84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r84 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Garcia KC]]
		+	[[Category: Jude KM]]
		+	[[Category: Miao Y]]

OCA: Protected "7r84" [edit=sysop:move=sysop]

OCA — Wed, 07 Jul 2021 08:58:18 GMT

Protected "7r84" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:58, 7 July 2021

OCA: New page: '''Unreleased structure''' The entry 7r84 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Jul 2021 08:58:17 GMT

New page: '''Unreleased structure''' The entry 7r84 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7r84 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]