5ova - Revision history

OCA at 01:25, 28 December 2023

2023-12-28T01:25:19Z

←Older revision		Revision as of 01:25, 28 December 2023
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	==Apo PDZ domain from rat Shank3==		==Apo PDZ domain from rat Shank3==
-	<StructureSection load='5ova' size='340' side='right' caption='[[5ova]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5ova' size='340' side='right'caption='[[5ova]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ova]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OVA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ova]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OVA FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Shank3~~, ~~Prosap2 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10116 Buffalo rat])~~</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]] 2.3Å</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=5ova FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ova OCA], [~~http~~://pdbe.org/5ova PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ova RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ova PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ova 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=5ova FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ova OCA], [https://pdbe.org/5ova PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ova RCSB], [https://www.ebi.ac.uk/pdbsum/5ova PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ova ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SHAN3_RAT SHAN3_RAT]] Seems to be an adapter protein in the postsynaptic density (PSD) of excitatory synapses that interconnects receptors of the postsynaptic membrane including NMDA-type and metabotropic glutamate receptors via complexes with GKAP/PSD-95 and Homer, respectively, and the actin-based cytoskeleton. May play a role in the structural and functional organization of the dendritic spine and synaptic junction.	+	[https://www.uniprot.org/uniprot/SHAN3_RAT SHAN3_RAT] Seems to be an adapter protein in the postsynaptic density (PSD) of excitatory synapses that interconnects receptors of the postsynaptic membrane including NMDA-type and metabotropic glutamate receptors via complexes with GKAP/PSD-95 and Homer, respectively, and the actin-based cytoskeleton. May play a role in the structural and functional organization of the dendritic spine and synaptic junction.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5ova" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ova" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Shank protein\|Shank protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Boeckers, T M~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Kursula, P~~]]	+	[[Category: Boeckers TM]]
-	[[Category: ~~Myllykoski, M~~]]	+	[[Category: Kursula P]]
-	[[Category: ~~Ponna, S K~~]]	+	[[Category: Myllykoski M]]
-	[[Category: ~~Pdz domain]]~~	+	[[Category: Ponna SK]]
-	~~[[Category: Peptide binding]]~~	+
-	~~[[Category: Post-synaptic density]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 06:05, 11 July 2018

2018-07-11T06:05:42Z

←Older revision		Revision as of 06:05, 11 July 2018
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	<StructureSection load='5ova' size='340' side='right' caption='[[5ova]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5ova' size='340' side='right' caption='[[5ova]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ova]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ova]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVA FirstGlance]. <br>
-	</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=5ova FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ova OCA], [http://pdbe.org/5ova PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ova RCSB], [http://www.ebi.ac.uk/pdbsum/5ova PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ova ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Shank3, Prosap2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=5ova FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ova OCA], [http://pdbe.org/5ova PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ova RCSB], [http://www.ebi.ac.uk/pdbsum/5ova PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ova ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Boeckers, T M]]		[[Category: Boeckers, T M]]
	[[Category: Kursula, P]]		[[Category: Kursula, P]]

OCA at 05:00, 8 March 2018

2018-03-08T05:00:10Z

←Older revision		Revision as of 05:00, 8 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5ova is ~~ON HOLD~~	+	==Apo PDZ domain from rat Shank3==
		+	<StructureSection load='5ova' size='340' side='right' caption='[[5ova]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ova]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVA FirstGlance]. <br>
		+	</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=5ova FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ova OCA], [http://pdbe.org/5ova PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ova RCSB], [http://www.ebi.ac.uk/pdbsum/5ova PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ova ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SHAN3_RAT SHAN3_RAT]] Seems to be an adapter protein in the postsynaptic density (PSD) of excitatory synapses that interconnects receptors of the postsynaptic membrane including NMDA-type and metabotropic glutamate receptors via complexes with GKAP/PSD-95 and Homer, respectively, and the actin-based cytoskeleton. May play a role in the structural and functional organization of the dendritic spine and synaptic junction.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Shank proteins are crucial scaffolding elements of the post-synaptic density (PSD). One of the best-characterized domains in Shank is the PDZ domain, which binds to C-terminal segments of several other PSD proteins. We carried out a detailed structural analysis of Shank3 PDZ domain-peptide complexes, in order to understand determinants of binding affinity towards different ligand proteins. Ligand peptides from four different proteins were cocrystallized with the Shank3 PDZ domain, and binding affinities were determined calorimetrically. In addition, to conserve class I interactions between the first and third C-terminal peptide residue and Shank3, side chain interactions of other residues in the peptide with the PDZ domain are important factors in defining affinity. Structural conservation suggests that the binding specificities of the PDZ domains from different Shanks are similar. Two conserved buried water molecules in PDZ domains may affect correct local folding of ligand recognition determinants. The solution structure of a tandem Shank3 construct containing the SH3 and PDZ domains showed that the two domains are close to each other, which could be of relevance, when recognizing and binding full target proteins. The SH3 domain did not affect the affinity of the PDZ domain towards short target peptides, and the schizophrenia-linked Shank3 mutation R536W in the linker between the domains had no effect on the structure or peptide interactions of the Shank3 SH3-PDZ unit. Our data show the spatial arrangement of two adjacent Shank domains and pinpoint affinity determinants for short PDZ domain ligands with limited sequence homology. This article is protected by copyright. All rights reserved.

-	~~Authors:~~ Ponna, S~~.K.~~, Myllykoski, M., Boeckers~~, T.M.~~, Kursula, P.	+	Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3.,Ponna SK, Ruskamo S, Myllykoski M, Keller C, Boeckers TM, Kursula P J Neurochem. 2018 Feb 23. doi: 10.1111/jnc.14322. PMID:29473168<ref>PMID:29473168</ref>

-	~~Description: Apo PDZ domain from rat Shank3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Boeckers, T~~.M]]~~	+	<div class="pdbe-citations 5ova" style="background-color:#fffaf0;"></div>
-	~~[[Category: Ponna, S.K]]~~	+	== References ==
-	~~[[Category: Myllykoski,~~ M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boeckers, T M]]
	[[Category: Kursula, P]]		[[Category: Kursula, P]]
		+	[[Category: Myllykoski, M]]
		+	[[Category: Ponna, S K]]
		+	[[Category: Pdz domain]]
		+	[[Category: Peptide binding]]
		+	[[Category: Post-synaptic density]]
		+	[[Category: Protein binding]]

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

2017-09-27T12:53:20Z

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

←Older revision

Revision as of 12:53, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ova is ON HOLD Authors: Ponna, S.K., Myllykoski, M., Boeckers, T.M., Kursula, P. Description: Apo PDZ domain from rat Shank3 [[Category: Unrelease...

2017-09-27T12:53:19Z

New page: '''Unreleased structure''' The entry 5ova is ON HOLD Authors: Ponna, S.K., Myllykoski, M., Boeckers, T.M., Kursula, P. Description: Apo PDZ domain from rat Shank3 [[Category: Unrelease...

New page

'''Unreleased structure'''

The entry 5ova is ON HOLD

Authors: Ponna, S.K., Myllykoski, M., Boeckers, T.M., Kursula, P.

Description: Apo PDZ domain from rat Shank3
[[Category: Unreleased Structures]]
[[Category: Boeckers, T.M]]
[[Category: Ponna, S.K]]
[[Category: Myllykoski, M]]
[[Category: Kursula, P]]