7cym - Revision history

OCA at 16:20, 29 November 2023

OCA — Wed, 29 Nov 2023 16:20:35 GMT

←Older revision		Revision as of 16:20, 29 November 2023
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	<StructureSection load='7cym' size='340' side='right'caption='[[7cym]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='7cym' size='340' side='right'caption='[[7cym]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7cym]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cym]] is a 2 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=7CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CYM 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</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]] 2.7Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDH17 ([https://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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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'>[https://proteopedia.org/fgij/fg.htm?mol=7cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cym OCA], [https://pdbe.org/7cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cym RCSB], [https://www.ebi.ac.uk/pdbsum/7cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cym 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=7cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cym OCA], [https://pdbe.org/7cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cym RCSB], [https://www.ebi.ac.uk/pdbsum/7cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CAD17_HUMAN CAD17_HUMAN]] Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. LI-cadherin may have a role in the morphological organization of liver and intestine. Involved in intestinal peptide transport.<ref>PMID:8153632</ref>	+	[https://www.uniprot.org/uniprot/CAD17_HUMAN CAD17_HUMAN] Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. LI-cadherin may have a role in the morphological organization of liver and intestine. Involved in intestinal peptide transport.<ref>PMID:8153632</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7cym" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7cym" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cadherin 3D structures\|Cadherin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Caaveiro~~, J M.M~~]]	+	[[Category: Caaveiro JMM]]
-	[[Category: Tsumoto, K]]	+	[[Category: Tsumoto K]]
-	[[Category: Yui, A]]	+	[[Category: Yui A]]
-	~~[[Category: Analytical ultracentrifugation]]~~	+
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Cell-adhesion]]~~	+
-	~~[[Category: Dimerization]]~~	+
-	~~[[Category: Li-cadherin]]~~	+
-	~~[[Category: Md simulation]]~~	+
-	~~[[Category: Protein chemistry]]~~	+
-	~~[[Category: Sax~~]]	+

OCA at 10:42, 5 January 2022

OCA — Wed, 05 Jan 2022 10:42:01 GMT

←Older revision		Revision as of 10:42, 5 January 2022
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	==Crystal structure of LI-Cadherin EC1-4==		==Crystal structure of LI-Cadherin EC1-4==
-	<StructureSection load='7cym' size='340' side='right'caption='[[7cym]]' scene=''>	+	<StructureSection load='7cym' size='340' side='right'caption='[[7cym]], [[Resolution\|resolution]] 2.70Å' 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=7CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cym]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CYM 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=7cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cym OCA], [https://pdbe.org/7cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cym RCSB], [https://www.ebi.ac.uk/pdbsum/7cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cym 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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDH17 ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cym OCA], [https://pdbe.org/7cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cym RCSB], [https://www.ebi.ac.uk/pdbsum/7cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cym ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CAD17_HUMAN CAD17_HUMAN]] Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. LI-cadherin may have a role in the morphological organization of liver and intestine. Involved in intestinal peptide transport.<ref>PMID:8153632</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LI-cadherin is a member of the cadherin superfamily, which encompasses a group of Ca(2+)-dependent cell adhesion proteins. The expression of LI-cadherin is observed on various types of cells in the human body, such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-cadherin is a promising target for gastric cancer imaging. However, since the cell adhesion mechanism of LI-cadherin has remained unknown, rational design of therapeutic molecules targeting this cadherin has been hampered. Here, we have studied the homodimerization mechanism of LI-cadherin. We report the crystal structure of the LI-cadherin homodimer containing its first four extracellular cadherin repeats (EC1-4). The EC1-4 homodimer exhibited a unique architecture different from that of other cadherins reported so far driven by the interactions between EC2 of one protein chain and EC4 of the other protein chain. The crystal structure also revealed that LI-cadherin possesses a noncanonical calcium ion-free linker between the EC2 and EC3 domains. Various biochemical techniques and molecular dynamics (MD) simulations were employed to elucidate the mechanism of homodimerization. We also showed that the formation of the homodimer observed in the crystal structure is necessary for LI-cadherin-dependent cell adhesion by performing cell aggregation assays. Taken together, our data provide structural insight necessary to advance the use of LI-cadherin as a target for imaging gastric cancer.
		+
		+	Mechanism of dimerization and structural features of human LI-cadherin.,Yui A, Caaveiro JMM, Kuroda D, Nakakido M, Nagatoishi S, Goda S, Maruno T, Uchiyama S, Tsumoto K J Biol Chem. 2021 Aug 5:101054. doi: 10.1016/j.jbc.2021.101054. PMID:34364873<ref>PMID:34364873</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7cym" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Caaveiro ~~JMM~~]]	+	[[Category: Caaveiro, J M.M]]
-	[[Category: Tsumoto K]]	+	[[Category: Tsumoto, K]]
-	[[Category: Yui A]]	+	[[Category: Yui, A]]
		+	[[Category: Analytical ultracentrifugation]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Cell-adhesion]]
		+	[[Category: Dimerization]]
		+	[[Category: Li-cadherin]]
		+	[[Category: Md simulation]]
		+	[[Category: Protein chemistry]]
		+	[[Category: Sax]]

OCA at 06:07, 18 August 2021

OCA — Wed, 18 Aug 2021 06:07:32 GMT

←Older revision		Revision as of 06:07, 18 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7cym is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of LI-Cadherin EC1-4==
-		+	<StructureSection load='7cym' size='340' side='right'caption='[[7cym]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CYM 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=7cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cym OCA], [https://pdbe.org/7cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cym RCSB], [https://www.ebi.ac.uk/pdbsum/7cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cym ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Caaveiro JMM]]
		+	[[Category: Tsumoto K]]
		+	[[Category: Yui A]]

OCA at 04:33, 7 October 2020

OCA — Wed, 07 Oct 2020 04:33:43 GMT

←Older revision		Revision as of 04:33, 7 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7cym is ON HOLD	+	The entry 7cym is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 09 Sep 2020 07:37:48 GMT

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

←Older revision

Revision as of 07:37, 9 September 2020

OCA: New page: '''Unreleased structure''' The entry 7cym is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 09 Sep 2020 07:37:46 GMT

New page: '''Unreleased structure''' The entry 7cym is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7cym is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]