6pkd - Revision history

OCA at 07:31, 11 October 2023

2023-10-11T07:31:14Z

←Older revision		Revision as of 07:31, 11 October 2023
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	<StructureSection load='6pkd' size='340' side='right'caption='[[6pkd]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6pkd' size='340' side='right'caption='[[6pkd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pkd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pkd]] 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=6PKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PKD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.9Å</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=6pkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkd OCA], [~~http~~://pdbe.org/6pkd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pkd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pkd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkd ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=6pkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkd OCA], [https://pdbe.org/6pkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pkd RCSB], [https://www.ebi.ac.uk/pdbsum/6pkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkd ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/MYOC_HUMAN MYOC_HUMAN]] Congenital glaucoma;Juvenile glaucoma. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. MYOC mutations may contribute to GLC3A via digenic inheritance with CYP1B1 and/or another locus associated with the disease (PubMed:15733270).<ref>PMID:15733270</ref>	+	[https://www.uniprot.org/uniprot/MYOC_HUMAN MYOC_HUMAN] Congenital glaucoma;Juvenile glaucoma. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. MYOC mutations may contribute to GLC3A via digenic inheritance with CYP1B1 and/or another locus associated with the disease (PubMed:15733270).<ref>PMID:15733270</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MYOC_HUMAN MYOC_HUMAN]] Secreted glycoprotein regulating the activation of different signaling pathways in adjacent cells to control different processes including cell adhesion, cell-matrix adhesion, cytoskeleton organization and cell migration. Promotes substrate adhesion, spreading and formation of focal contacts. Negatively regulates cell-matrix adhesion and stress fiber assembly through Rho protein signal transduction. Modulates the organization of actin cytoskeleton by stimulating the formation of stress fibers through interactions with components of Wnt signaling pathways. Promotes cell migration through activation of PTK2 and the downstream phosphatidylinositol 3-kinase signaling. Plays a role in bone formation and promotes osteoblast differentiation in a dose-dependent manner through mitogen-activated protein kinase signaling. Mediates myelination in the peripheral nervous system through ERBB2/ERBB3 signaling. Plays a role as a regulator of muscle hypertrophy through the components of dystrophin-associated protein complex. Involved in positive regulation of mitochondrial depolarization. Plays a role in neurite outgrowth. May participate in the obstruction of fluid outflow in the trabecular meshwork.<ref>PMID:17516541</ref> <ref>PMID:17984096</ref> <ref>PMID:18855004</ref> <ref>PMID:19188438</ref> <ref>PMID:19959812</ref> <ref>PMID:21656515</ref> <ref>PMID:23629661</ref> <ref>PMID:23897819</ref>	+	[https://www.uniprot.org/uniprot/MYOC_HUMAN MYOC_HUMAN] Secreted glycoprotein regulating the activation of different signaling pathways in adjacent cells to control different processes including cell adhesion, cell-matrix adhesion, cytoskeleton organization and cell migration. Promotes substrate adhesion, spreading and formation of focal contacts. Negatively regulates cell-matrix adhesion and stress fiber assembly through Rho protein signal transduction. Modulates the organization of actin cytoskeleton by stimulating the formation of stress fibers through interactions with components of Wnt signaling pathways. Promotes cell migration through activation of PTK2 and the downstream phosphatidylinositol 3-kinase signaling. Plays a role in bone formation and promotes osteoblast differentiation in a dose-dependent manner through mitogen-activated protein kinase signaling. Mediates myelination in the peripheral nervous system through ERBB2/ERBB3 signaling. Plays a role as a regulator of muscle hypertrophy through the components of dystrophin-associated protein complex. Involved in positive regulation of mitochondrial depolarization. Plays a role in neurite outgrowth. May participate in the obstruction of fluid outflow in the trabecular meshwork.<ref>PMID:17516541</ref> <ref>PMID:17984096</ref> <ref>PMID:18855004</ref> <ref>PMID:19188438</ref> <ref>PMID:19959812</ref> <ref>PMID:21656515</ref> <ref>PMID:23629661</ref> <ref>PMID:23897819</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hill~~, S E~~]]	+	[[Category: Hill SE]]
-	[[Category: Lieberman~~, R L]]~~	+	[[Category: Lieberman RL]]
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Propeller~~]]	+

OCA at 11:47, 13 November 2019

2019-11-13T11:47:37Z

←Older revision		Revision as of 11:47, 13 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~6pkd~~ is ~~ON HOLD~~	+	==Myocilin OLF mutant N428D/D478H==
		+	<StructureSection load='6pkd' size='340' side='right'caption='[[6pkd]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6pkd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=6pkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkd OCA], [http://pdbe.org/6pkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkd RCSB], [http://www.ebi.ac.uk/pdbsum/6pkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkd ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/MYOC_HUMAN MYOC_HUMAN]] Congenital glaucoma;Juvenile glaucoma. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. MYOC mutations may contribute to GLC3A via digenic inheritance with CYP1B1 and/or another locus associated with the disease (PubMed:15733270).<ref>PMID:15733270</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MYOC_HUMAN MYOC_HUMAN]] Secreted glycoprotein regulating the activation of different signaling pathways in adjacent cells to control different processes including cell adhesion, cell-matrix adhesion, cytoskeleton organization and cell migration. Promotes substrate adhesion, spreading and formation of focal contacts. Negatively regulates cell-matrix adhesion and stress fiber assembly through Rho protein signal transduction. Modulates the organization of actin cytoskeleton by stimulating the formation of stress fibers through interactions with components of Wnt signaling pathways. Promotes cell migration through activation of PTK2 and the downstream phosphatidylinositol 3-kinase signaling. Plays a role in bone formation and promotes osteoblast differentiation in a dose-dependent manner through mitogen-activated protein kinase signaling. Mediates myelination in the peripheral nervous system through ERBB2/ERBB3 signaling. Plays a role as a regulator of muscle hypertrophy through the components of dystrophin-associated protein complex. Involved in positive regulation of mitochondrial depolarization. Plays a role in neurite outgrowth. May participate in the obstruction of fluid outflow in the trabecular meshwork.<ref>PMID:17516541</ref> <ref>PMID:17984096</ref> <ref>PMID:18855004</ref> <ref>PMID:19188438</ref> <ref>PMID:19959812</ref> <ref>PMID:21656515</ref> <ref>PMID:23629661</ref> <ref>PMID:23897819</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Olfactomedins are a family of modular proteins found in multicellular organisms that all contain five-bladed beta-propeller olfactomedin (OLF) domains. In support of differential functions for the OLF propeller, the available crystal structures reveal that only some OLF domains harbor an internal calcium-binding site with ligands derived from a triad of residues. For the myocilin OLF domain (myoc-OLF), ablation of the ion-binding site (triad Asp, Asn, Asp) by altering the coordinating residues affects the stability and overall structure, in one case leading to misfolding and glaucoma. Bioinformatics analysis reveals a variety of triads with possible ion-binding characteristics lurking in OLF domains in invertebrate chordates such as Arthropoda (Asp-Glu-Ser), Nematoda (Asp-Asp-His) and Echinodermata (Asp-Glu-Lys). To test ion binding and to extend the observed connection between ion binding and distal structural rearrangements, consensus triads from these phyla were installed in the myoc-OLF. All three protein variants exhibit wild-type-like or better stability, but their calcium-binding properties differ, concomitant with new structural deviations from wild-type myoc-OLF. Taken together, the results indicate that calcium binding is not intrinsically destabilizing to myoc-OLF or required to observe a well ordered side helix, and that ion binding is a differential feature that may underlie the largely elusive biological function of OLF propellers.

-	~~Authors~~:	+	Calcium-ligand variants of the myocilin olfactomedin propeller selected from invertebrate phyla reveal cross-talk with N-terminal blade and surface helices.,Hill SE, Cho H, Raut P, Lieberman RL Acta Crystallogr D Struct Biol. 2019 Sep 1;75(Pt 9):817-824. doi:, 10.1107/S205979831901074X. Epub 2019 Aug 22. PMID:31478904<ref>PMID:31478904</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6pkd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hill, S E]]
		+	[[Category: Lieberman, R L]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Propeller]]

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

2019-07-10T04:11:03Z

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

←Older revision

Revision as of 04:11, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pkd is ON HOLD Authors: Description: Category: Unreleased Structures

2019-07-10T04:11:01Z

New page: '''Unreleased structure''' The entry 6pkd is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pkd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]