6x3a - Revision history

OCA at 07:10, 3 April 2024

OCA — Wed, 03 Apr 2024 07:10:42 GMT

←Older revision		Revision as of 07:10, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='6x3a' size='340' side='right'caption='[[6x3a]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='6x3a' size='340' side='right'caption='[[6x3a]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6x3a]] is a 1 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=6X3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6x3a]] 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=6X3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X3A FirstGlance]. <br>
-	</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>~~</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]] 1.77Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PTPRD ([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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48]~~ </~~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=6x3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x3a OCA], [https://pdbe.org/6x3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x3a RCSB], [https://www.ebi.ac.uk/pdbsum/6x3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x3a 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=6x3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x3a OCA], [https://pdbe.org/6x3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x3a RCSB], [https://www.ebi.ac.uk/pdbsum/6x3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x3a ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/PTPRD_HUMAN PTPRD_HUMAN]
-	The type IIa family of receptor protein tyrosine phosphatases (RPTPs), including Lar, RPTPsigma and RPTPdelta, are well-studied in coordinating actin cytoskeletal rearrangements during axon guidance and synaptogenesis. To determine whether this regulation is conserved in other tissues, interdisciplinary approaches were utilized to study Lar-RPTPs in the Drosophila musculature. Here we find that the single fly ortholog, Drosophila Lar (Dlar), is localized to the muscle costamere and that a decrease in Dlar causes aberrant sarcomeric patterning, deficits in larval locomotion, and integrin mislocalization. Sequence analysis uncovered an evolutionarily conserved Lys-Gly-Asp (KGD) signature in the extracellular region of Dlar. Since this tripeptide sequence is similar to the integrin-binding Arg-Gly-Asp (RGD) motif, we tested the hypothesis that Dlar directly interacts with integrin proteins. However, structural analyses of the fibronectin type III domains of Dlar and two vertebrate orthologs that include this conserved motif indicate that this KGD tripeptide is not accessible and thus unlikely to mediate physical interactions with integrins. These results, together with the proteomics identification of basement membrane (BM) proteins as potential ligands for type IIa RPTPs, suggest a complex network of protein interactions in the extracellular space that may mediate Lar function and/or signaling in muscle tissue.	+
-		+
-	~~Complex protein interactions mediate Drosophila Lar function in muscle tissue.,Kawakami J, Brooks D, Zalmai R, Hartson SD, Bouyain S, Geisbrecht ER PLoS One. 2022 May 27;17(5)~~:~~e0269037. doi: 10.1371~~/~~journal.pone.0269037., eCollection 2022. PMID:35622884<ref>PMID:35622884<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6x3a" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]		*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Protein-tyrosine-phosphatase]]~~	+	[[Category: Bouyain S]]
-	[[Category: Bouyain, S]]	+	[[Category: Kawakami JE]]
-	[[Category: Kawakami~~, J E]]~~	+
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Fibronectin type iii]]~~	+
-	~~[[Category: Receptor protein tyrosine phosphatase~~]]	+

OCA at 09:50, 22 June 2022

OCA — Wed, 22 Jun 2022 09:50:55 GMT

←Older revision		Revision as of 09:50, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of the FN4-FN6 domains of human PTPRD==		==Crystal structure of the FN4-FN6 domains of human PTPRD==
-	<StructureSection load='6x3a' size='340' side='right'caption='[[6x3a]]' scene=''>	+	<StructureSection load='6x3a' size='340' side='right'caption='[[6x3a]], [[Resolution\|resolution]] 1.77Å' 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=6X3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6x3a]] is a 1 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=6X3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X3A 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=6x3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x3a OCA], [https://pdbe.org/6x3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x3a RCSB], [https://www.ebi.ac.uk/pdbsum/6x3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x3a 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=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PTPRD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=6x3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x3a OCA], [https://pdbe.org/6x3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x3a RCSB], [https://www.ebi.ac.uk/pdbsum/6x3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x3a ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The type IIa family of receptor protein tyrosine phosphatases (RPTPs), including Lar, RPTPsigma and RPTPdelta, are well-studied in coordinating actin cytoskeletal rearrangements during axon guidance and synaptogenesis. To determine whether this regulation is conserved in other tissues, interdisciplinary approaches were utilized to study Lar-RPTPs in the Drosophila musculature. Here we find that the single fly ortholog, Drosophila Lar (Dlar), is localized to the muscle costamere and that a decrease in Dlar causes aberrant sarcomeric patterning, deficits in larval locomotion, and integrin mislocalization. Sequence analysis uncovered an evolutionarily conserved Lys-Gly-Asp (KGD) signature in the extracellular region of Dlar. Since this tripeptide sequence is similar to the integrin-binding Arg-Gly-Asp (RGD) motif, we tested the hypothesis that Dlar directly interacts with integrin proteins. However, structural analyses of the fibronectin type III domains of Dlar and two vertebrate orthologs that include this conserved motif indicate that this KGD tripeptide is not accessible and thus unlikely to mediate physical interactions with integrins. These results, together with the proteomics identification of basement membrane (BM) proteins as potential ligands for type IIa RPTPs, suggest a complex network of protein interactions in the extracellular space that may mediate Lar function and/or signaling in muscle tissue.
		+
		+	Complex protein interactions mediate Drosophila Lar function in muscle tissue.,Kawakami J, Brooks D, Zalmai R, Hartson SD, Bouyain S, Geisbrecht ER PLoS One. 2022 May 27;17(5):e0269037. doi: 10.1371/journal.pone.0269037., eCollection 2022. PMID:35622884<ref>PMID:35622884</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6x3a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bouyain S]]	+	[[Category: Protein-tyrosine-phosphatase]]
-	[[Category: Kawakami JE]]	+	[[Category: Bouyain, S]]
		+	[[Category: Kawakami, J E]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Fibronectin type iii]]
		+	[[Category: Receptor protein tyrosine phosphatase]]

OCA at 09:15, 26 May 2021

OCA — Wed, 26 May 2021 09:15:59 GMT

←Older revision		Revision as of 09:15, 26 May 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6x3a is ON HOLD until Paper Publication~~	+	==Crystal structure of the FN4-FN6 domains of human PTPRD==
-		+	<StructureSection load='6x3a' size='340' side='right'caption='[[6x3a]]' scene=''>
-	~~Authors: Bouyain, S., Kawakami, J.E.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6X3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X3A FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the FN4-FN6 domains of human PTPRD	+	</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=6x3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x3a OCA], [https://pdbe.org/6x3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x3a RCSB], [https://www.ebi.ac.uk/pdbsum/6x3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x3a ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Kawakami~~, J.E]]	+	__TOC__
-	[[Category: Bouyain, S]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bouyain S]]
		+	[[Category: Kawakami JE]]

OCA at 05:10, 3 June 2020

OCA — Wed, 03 Jun 2020 05:10:53 GMT

←Older revision		Revision as of 05:10, 3 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6x3a is ON HOLD	+	The entry 6x3a is ON HOLD until Paper Publication

	Authors: Bouyain, S., Kawakami, J.E.		Authors: Bouyain, S., Kawakami, J.E.

OCA: Protected "6x3a" [edit=sysop:move=sysop]

OCA — Wed, 27 May 2020 04:57:27 GMT

Protected "6x3a" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:57, 27 May 2020

OCA: New page: '''Unreleased structure''' The entry 6x3a is ON HOLD Authors: Bouyain, S., Kawakami, J.E. Description: Crystal structure of the FN4-FN6 domains of human PTPRD [[Category: Unreleased St...

OCA — Wed, 27 May 2020 04:57:25 GMT

New page: '''Unreleased structure''' The entry 6x3a is ON HOLD Authors: Bouyain, S., Kawakami, J.E. Description: Crystal structure of the FN4-FN6 domains of human PTPRD [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6x3a is ON HOLD

Authors: Bouyain, S., Kawakami, J.E.

Description: Crystal structure of the FN4-FN6 domains of human PTPRD
[[Category: Unreleased Structures]]
[[Category: Kawakami, J.E]]
[[Category: Bouyain, S]]