5o0p - Revision history

OCA at 12:19, 22 November 2023

OCA — Wed, 22 Nov 2023 12:19:34 GMT

←Older revision		Revision as of 12:19, 22 November 2023
Line 1:		Line 1:

	==Deglycosylated Nogo Receptor with native disulfide structure 6==		==Deglycosylated Nogo Receptor with native disulfide structure 6==
-	<StructureSection load='5o0p' size='340' side='right' caption='[[5o0p]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5o0p' size='340' side='right'caption='[[5o0p]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o0p]] is a 2 chain structure with sequence from [~~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=5O0P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o0p]] 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=5O0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O0P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rtn4r, Ngr1, Nogor ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5o0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0p OCA], [~~http~~://pdbe.org/5o0p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o0p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o0p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0p 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=5o0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0p OCA], [https://pdbe.org/5o0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o0p RCSB], [https://www.ebi.ac.uk/pdbsum/5o0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RTN4R_MOUSE RTN4R_MOUSE]] Receptor for RTN4, OMG and MAG (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:18411262, PubMed:22923615). Functions as receptor for the sialylated gangliosides GT1b and GM1 (PubMed:18411262). Besides, functions as receptor for chondroitin sulfate proteoglycans (PubMed:22406547). Can also bind heparin (PubMed:22406547). Intracellular signaling cascades are triggered via the coreceptor NGFR (By similarity). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:22325200). Mediates axonal growth inhibition (By similarity). Mediates axonal growth inhibition and plays a role in regulating axon regeneration and neuronal plasticity in the adult central nervous system (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:22923615). Plays a role in postnatal brain development (PubMed:27339102). Required for normal axon migration across the brain midline and normal formation of the corpus callosum (PubMed:27339102). Protects motoneurons against apoptosis; protection against apoptosis is probably mediated via interaction with MAG (PubMed:26335717). Acts in conjunction with RTN4 and LINGO1 in regulating neuronal precursor cell motility during cortical development (PubMed:20093372). Like other family members, plays a role in restricting the number dendritic spines and the number of synapses that are formed during brain development (PubMed:22325200).[UniProtKB:Q9BZR6]<ref>PMID:11201742</ref> <ref>PMID:12089450</ref> <ref>PMID:15504325</ref> <ref>PMID:20093372</ref> <ref>PMID:22325200</ref> <ref>PMID:22406547</ref> <ref>PMID:22923615</ref> <ref>PMID:26335717</ref> <ref>PMID:27339102</ref>	+	[https://www.uniprot.org/uniprot/RTN4R_MOUSE RTN4R_MOUSE] Receptor for RTN4, OMG and MAG (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:18411262, PubMed:22923615). Functions as receptor for the sialylated gangliosides GT1b and GM1 (PubMed:18411262). Besides, functions as receptor for chondroitin sulfate proteoglycans (PubMed:22406547). Can also bind heparin (PubMed:22406547). Intracellular signaling cascades are triggered via the coreceptor NGFR (By similarity). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:22325200). Mediates axonal growth inhibition (By similarity). Mediates axonal growth inhibition and plays a role in regulating axon regeneration and neuronal plasticity in the adult central nervous system (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:22923615). Plays a role in postnatal brain development (PubMed:27339102). Required for normal axon migration across the brain midline and normal formation of the corpus callosum (PubMed:27339102). Protects motoneurons against apoptosis; protection against apoptosis is probably mediated via interaction with MAG (PubMed:26335717). Acts in conjunction with RTN4 and LINGO1 in regulating neuronal precursor cell motility during cortical development (PubMed:20093372). Like other family members, plays a role in restricting the number dendritic spines and the number of synapses that are formed during brain development (PubMed:22325200).[UniProtKB:Q9BZR6]<ref>PMID:11201742</ref> <ref>PMID:12089450</ref> <ref>PMID:15504325</ref> <ref>PMID:20093372</ref> <ref>PMID:22325200</ref> <ref>PMID:22406547</ref> <ref>PMID:22923615</ref> <ref>PMID:26335717</ref> <ref>PMID:27339102</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Janssen, B J.C~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Pronker, M F~~]]	+	[[Category: Janssen BJC]]
-	[[Category: ~~Disulfide structure]]~~	+	[[Category: Pronker MF]]
-	~~[[Category: Leucine-rich repeat domain]]~~	+
-	~~[[Category: Nervous system]]~~	+
-	~~[[Category: Signaling]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 10:12, 15 November 2017

OCA — Wed, 15 Nov 2017 10:12:09 GMT

←Older revision		Revision as of 10:12, 15 November 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RTN4R_MOUSE RTN4R_MOUSE]] Receptor for RTN4, OMG and MAG (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:18411262, PubMed:22923615). Functions as receptor for the sialylated gangliosides GT1b and GM1 (PubMed:18411262). Besides, functions as receptor for chondroitin sulfate proteoglycans (PubMed:22406547). Can also bind heparin (PubMed:22406547). Intracellular signaling cascades are triggered via the coreceptor NGFR (By similarity). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:22325200). Mediates axonal growth inhibition (By similarity). Mediates axonal growth inhibition and plays a role in regulating axon regeneration and neuronal plasticity in the adult central nervous system (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:22923615). Plays a role in postnatal brain development (PubMed:27339102). Required for normal axon migration across the brain midline and normal formation of the corpus callosum (PubMed:27339102). Protects motoneurons against apoptosis; protection against apoptosis is probably mediated via interaction with MAG (PubMed:26335717). Acts in conjunction with RTN4 and LINGO1 in regulating neuronal precursor cell motility during cortical development (PubMed:20093372). Like other family members, plays a role in restricting the number dendritic spines and the number of synapses that are formed during brain development (PubMed:22325200).[UniProtKB:Q9BZR6]<ref>PMID:11201742</ref> <ref>PMID:12089450</ref> <ref>PMID:15504325</ref> <ref>PMID:20093372</ref> <ref>PMID:22325200</ref> <ref>PMID:22406547</ref> <ref>PMID:22923615</ref> <ref>PMID:26335717</ref> <ref>PMID:27339102</ref>		[[http://www.uniprot.org/uniprot/RTN4R_MOUSE RTN4R_MOUSE]] Receptor for RTN4, OMG and MAG (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:18411262, PubMed:22923615). Functions as receptor for the sialylated gangliosides GT1b and GM1 (PubMed:18411262). Besides, functions as receptor for chondroitin sulfate proteoglycans (PubMed:22406547). Can also bind heparin (PubMed:22406547). Intracellular signaling cascades are triggered via the coreceptor NGFR (By similarity). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:22325200). Mediates axonal growth inhibition (By similarity). Mediates axonal growth inhibition and plays a role in regulating axon regeneration and neuronal plasticity in the adult central nervous system (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:22923615). Plays a role in postnatal brain development (PubMed:27339102). Required for normal axon migration across the brain midline and normal formation of the corpus callosum (PubMed:27339102). Protects motoneurons against apoptosis; protection against apoptosis is probably mediated via interaction with MAG (PubMed:26335717). Acts in conjunction with RTN4 and LINGO1 in regulating neuronal precursor cell motility during cortical development (PubMed:20093372). Like other family members, plays a role in restricting the number dendritic spines and the number of synapses that are formed during brain development (PubMed:22325200).[UniProtKB:Q9BZR6]<ref>PMID:11201742</ref> <ref>PMID:12089450</ref> <ref>PMID:15504325</ref> <ref>PMID:20093372</ref> <ref>PMID:22325200</ref> <ref>PMID:22406547</ref> <ref>PMID:22923615</ref> <ref>PMID:26335717</ref> <ref>PMID:27339102</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Nogo Receptor (NgR) is a glycophosphatidylinositol-anchored cell-surface protein and is a receptor for three myelin-associated inhibitors of regeneration: myelin-associated glycoprotein, Nogo66 and oligodendrocyte myelin glycoprotein. In combination with different co-receptors, NgR mediates signalling that reduces neuronal plasticity. The available structures of the NgR ligand-binding leucine-rich repeat (LRR) domain have an artificial disulfide pattern owing to truncated C-terminal construct boundaries. NgR has previously been shown to self-associate via its LRR domain, but the structural basis of this interaction remains elusive. Here, crystal structures of the NgR LRR with a longer C-terminal segment and a native disulfide pattern are presented. An additional C-terminal loop proximal to the C-terminal LRR cap is stabilized by two newly formed disulfide bonds, but is otherwise mostly unstructured in the absence of any stabilizing interactions. NgR crystallized in six unique crystal forms, three of which share a crystal-packing interface. NgR crystal-packing interfaces from all eight unique crystal forms are compared in order to explore how NgR could self-interact on the neuronal plasma membrane.
		+
		+	Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction.,Pronker MF, Tas RP, Vlieg HC, Janssen BJC Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):860-876. doi:, 10.1107/S2059798317013791. Epub 2017 Oct 19. PMID:29095159<ref>PMID:29095159</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5o0p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:19, 8 November 2017

OCA — Wed, 08 Nov 2017 10:19:34 GMT

←Older revision		Revision as of 10:19, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='5o0p' size='340' side='right' caption='[[5o0p]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5o0p' size='340' side='right' caption='[[5o0p]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o0p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o0p]] is a 2 chain structure with sequence from [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=5O0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O0P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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">Rtn4r, Ngr1, Nogor ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5o0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0p OCA], [http://pdbe.org/5o0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o0p RCSB], [http://www.ebi.ac.uk/pdbsum/5o0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0p 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=5o0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0p OCA], [http://pdbe.org/5o0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o0p RCSB], [http://www.ebi.ac.uk/pdbsum/5o0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0p ProSAT]</span></td></tr>
	</table>		</table>
Line 13:		Line 14:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Janssen, B J.C]]		[[Category: Janssen, B J.C]]
	[[Category: Pronker, M F]]		[[Category: Pronker, M F]]

OCA at 07:10, 18 October 2017

OCA — Wed, 18 Oct 2017 07:10:35 GMT

←Older revision		Revision as of 07:10, 18 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o0p is ~~ON HOLD~~	+	==Deglycosylated Nogo Receptor with native disulfide structure 6==
-		+	<StructureSection load='5o0p' size='340' side='right' caption='[[5o0p]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5o0p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O0P FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5o0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o0p OCA], [http://pdbe.org/5o0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o0p RCSB], [http://www.ebi.ac.uk/pdbsum/5o0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o0p ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RTN4R_MOUSE RTN4R_MOUSE]] Receptor for RTN4, OMG and MAG (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:18411262, PubMed:22923615). Functions as receptor for the sialylated gangliosides GT1b and GM1 (PubMed:18411262). Besides, functions as receptor for chondroitin sulfate proteoglycans (PubMed:22406547). Can also bind heparin (PubMed:22406547). Intracellular signaling cascades are triggered via the coreceptor NGFR (By similarity). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:22325200). Mediates axonal growth inhibition (By similarity). Mediates axonal growth inhibition and plays a role in regulating axon regeneration and neuronal plasticity in the adult central nervous system (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:22923615). Plays a role in postnatal brain development (PubMed:27339102). Required for normal axon migration across the brain midline and normal formation of the corpus callosum (PubMed:27339102). Protects motoneurons against apoptosis; protection against apoptosis is probably mediated via interaction with MAG (PubMed:26335717). Acts in conjunction with RTN4 and LINGO1 in regulating neuronal precursor cell motility during cortical development (PubMed:20093372). Like other family members, plays a role in restricting the number dendritic spines and the number of synapses that are formed during brain development (PubMed:22325200).[UniProtKB:Q9BZR6]<ref>PMID:11201742</ref> <ref>PMID:12089450</ref> <ref>PMID:15504325</ref> <ref>PMID:20093372</ref> <ref>PMID:22325200</ref> <ref>PMID:22406547</ref> <ref>PMID:22923615</ref> <ref>PMID:26335717</ref> <ref>PMID:27339102</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Janssen, B J.C]]
		+	[[Category: Pronker, M F]]
		+	[[Category: Disulfide structure]]
		+	[[Category: Leucine-rich repeat domain]]
		+	[[Category: Nervous system]]
		+	[[Category: Signaling]]
		+	[[Category: Signaling protein]]

OCA: Protected "5o0p" [edit=sysop:move=sysop]

OCA — Wed, 24 May 2017 10:06:19 GMT

Protected "5o0p" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:06, 24 May 2017

OCA: New page: '''Unreleased structure''' The entry 5o0p is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 May 2017 10:06:18 GMT

New page: '''Unreleased structure''' The entry 5o0p is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5o0p is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]