5k6v - Revision history

OCA at 06:54, 3 April 2024

OCA — Wed, 03 Apr 2024 06:54:48 GMT

←Older revision		Revision as of 06:54, 3 April 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SDK1_MOUSE SDK1_MOUSE] Adhesion molecule that promotes lamina-specific synaptic connections in the retina. Expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions.[UniProtKB:Q8AV58]		[https://www.uniprot.org/uniprot/SDK1_MOUSE SDK1_MOUSE] Adhesion molecule that promotes lamina-specific synaptic connections in the retina. Expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions.[UniProtKB:Q8AV58]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlies their neuronal targeting function. Here we report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1-4), arranged in a horseshoe conformation. These Ig1-4 horseshoes interact in a novel back-to-back orientation in both homodimers through Ig1:Ig2, Ig1:Ig1 and Ig3:Ig4 interactions. Structure-guided mutagenesis results show that this canonical dimer is required for both Sdk-mediated cell aggregation (via trans interactions) and Sdk clustering in isolated cells (via cis interactions). Sdk1/Sdk2 recognition specificity is encoded across Ig1-4, with Ig1-2 conferring the majority of binding affinity and differential specificity. We suggest that competition between cis and trans interactions provides a novel mechanism to sharpen the specificity of cell-cell interactions.
-
-	Molecular basis of sidekick-mediated cell-cell adhesion and specificity.,Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsen G, Sergeeva AP, Honig B, Sanes JR, Shapiro L Elife. 2016 Sep 19;5. pii: e19058. doi: 10.7554/eLife.19058. PMID:27644106<ref>PMID:27644106</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5k6v" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:42, 27 September 2023

OCA — Wed, 27 Sep 2023 10:42:03 GMT

←Older revision		Revision as of 10:42, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5k6v' size='340' side='right'caption='[[5k6v]], [[Resolution\|resolution]] 3.21Å' scene=''>		<StructureSection load='5k6v' size='340' side='right'caption='[[5k6v]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k6v]] is a 1 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=5K6V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k6v]] is a 1 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=5K6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K6V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.208Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k6u\|5k6u]], [[5k6w\|5k6w]], [[5k6x\|5k6x]], [[5k6y\|5k6y]], [[5k6z\|5k6z]], [[5k70\|5k70]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Sdk1 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6v OCA], [https://pdbe.org/5k6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k6v RCSB], [https://www.ebi.ac.uk/pdbsum/5k6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6v 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=5k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6v OCA], [~~http~~://pdbe.org/5k6v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k6v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k6v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SDK1_MOUSE SDK1_MOUSE]] Adhesion molecule that promotes lamina-specific synaptic connections in the retina. Expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions.[UniProtKB:Q8AV58]	+	[https://www.uniprot.org/uniprot/SDK1_MOUSE SDK1_MOUSE] Adhesion molecule that promotes lamina-specific synaptic connections in the retina. Expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions.[UniProtKB:Q8AV58]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Goodman~~, K M~~]]	+	[[Category: Goodman KM]]
-	[[Category: Honig, B]]	+	[[Category: Honig B]]
-	[[Category: Jin, X]]	+	[[Category: Jin X]]
-	[[Category: Mannepalli, S]]	+	[[Category: Mannepalli S]]
-	[[Category: Shapiro, L]]	+	[[Category: Shapiro L]]
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Immunoglobulin~~]]	+

OCA at 09:23, 1 July 2020

OCA — Wed, 01 Jul 2020 09:23:35 GMT

←Older revision		Revision as of 09:23, 1 July 2020
Line 1:		Line 1:

	==Sidekick-1 immunoglobulin domains 1-4, crystal form 2==		==Sidekick-1 immunoglobulin domains 1-4, crystal form 2==
-	<StructureSection load='5k6v' size='340' side='right' caption='[[5k6v]], [[Resolution\|resolution]] 3.21Å' scene=''>	+	<StructureSection load='5k6v' size='340' side='right'caption='[[5k6v]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k6v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K6V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k6v]] is a 1 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=5K6V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K6V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k6u\|5k6u]], [[5k6w\|5k6w]], [[5k6x\|5k6x]], [[5k6y\|5k6y]], [[5k6z\|5k6z]], [[5k70\|5k70]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k6u\|5k6u]], [[5k6w\|5k6w]], [[5k6x\|5k6x]], [[5k6y\|5k6y]], [[5k6z\|5k6z]], [[5k70\|5k70]]</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=5k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6v OCA], [http://pdbe.org/5k6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6v RCSB], [http://www.ebi.ac.uk/pdbsum/5k6v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6v ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Sdk1 ([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://proteopedia.org/fgij/fg.htm?mol=5k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6v OCA], [http://pdbe.org/5k6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6v RCSB], [http://www.ebi.ac.uk/pdbsum/5k6v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Goodman, K M]]		[[Category: Goodman, K M]]
	[[Category: Honig, B]]		[[Category: Honig, B]]

OCA at 16:56, 3 October 2016

OCA — Mon, 03 Oct 2016 16:56:27 GMT

←Older revision		Revision as of 16:56, 3 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k6v is ~~ON HOLD until Paper~~ Publication	+	==Sidekick-1 immunoglobulin domains 1-4, crystal form 2==
		+	<StructureSection load='5k6v' size='340' side='right' caption='[[5k6v]], [[Resolution\|resolution]] 3.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k6v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K6V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k6u\|5k6u]], [[5k6w\|5k6w]], [[5k6x\|5k6x]], [[5k6y\|5k6y]], [[5k6z\|5k6z]], [[5k70\|5k70]]</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=5k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k6v OCA], [http://pdbe.org/5k6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k6v RCSB], [http://www.ebi.ac.uk/pdbsum/5k6v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k6v ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SDK1_MOUSE SDK1_MOUSE]] Adhesion molecule that promotes lamina-specific synaptic connections in the retina. Expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions.[UniProtKB:Q8AV58]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlies their neuronal targeting function. Here we report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1-4), arranged in a horseshoe conformation. These Ig1-4 horseshoes interact in a novel back-to-back orientation in both homodimers through Ig1:Ig2, Ig1:Ig1 and Ig3:Ig4 interactions. Structure-guided mutagenesis results show that this canonical dimer is required for both Sdk-mediated cell aggregation (via trans interactions) and Sdk clustering in isolated cells (via cis interactions). Sdk1/Sdk2 recognition specificity is encoded across Ig1-4, with Ig1-2 conferring the majority of binding affinity and differential specificity. We suggest that competition between cis and trans interactions provides a novel mechanism to sharpen the specificity of cell-cell interactions.

-	~~Authors~~:	+	Molecular basis of sidekick-mediated cell-cell adhesion and specificity.,Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsen G, Sergeeva AP, Honig B, Sanes JR, Shapiro L Elife. 2016 Sep 19;5. pii: e19058. doi: 10.7554/eLife.19058. PMID:27644106<ref>PMID:27644106</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k6v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Goodman, K M]]
		+	[[Category: Honig, B]]
		+	[[Category: Jin, X]]
		+	[[Category: Mannepalli, S]]
		+	[[Category: Shapiro, L]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Immunoglobulin]]

OCA at 13:29, 20 June 2016

OCA — Mon, 20 Jun 2016 13:29:28 GMT

←Older revision		Revision as of 13:29, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k6v is ON HOLD	+	The entry 5k6v is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5k6v" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:24:10 GMT

Protected "5k6v" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:24, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k6v is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:24:08 GMT

New page: '''Unreleased structure''' The entry 5k6v is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k6v is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]