5w72 - Revision history

OCA at 10:05, 15 November 2023

2023-11-15T10:05:09Z

←Older revision		Revision as of 10:05, 15 November 2023
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	==Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography==		==Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography==
-	<StructureSection load='5w72' size='340' side='right'caption='[[5w72~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5w72' size='340' side='right'caption='[[5w72]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w72]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W72 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W72 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w72]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W72 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=AZH:AZIDOHOMOALANINE'>AZH</scene~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Dlg4, Dlgh4, Psd95 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZH:AZIDOHOMOALANINE'>AZH</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=5w72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w72 OCA], [~~http~~://pdbe.org/5w72 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w72 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w72 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w72 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=5w72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w72 OCA], [https://pdbe.org/5w72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w72 RCSB], [https://www.ebi.ac.uk/pdbsum/5w72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w72 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DLG4_RAT DLG4_RAT]] Interacts with the cytoplasmic tail of NMDA receptor subunits and shaker-type potassium channels. Required for synaptic plasticity associated with NMDA receptor signaling. Overexpression or depletion of DLG4 changes the ratio of excitatory to inhibitory synapses in hippocampal neurons. May reduce the amplitude of ASIC3 acid-evoked currents by retaining the channel intracellularly. May regulate the intracellular trafficking of ADR1B.<ref>PMID:15317815</ref> <ref>PMID:15358863</ref>	+	[https://www.uniprot.org/uniprot/DLG4_RAT DLG4_RAT] Interacts with the cytoplasmic tail of NMDA receptor subunits and shaker-type potassium channels. Required for synaptic plasticity associated with NMDA receptor signaling. Overexpression or depletion of DLG4 changes the ratio of excitatory to inhibitory synapses in hippocampal neurons. May reduce the amplitude of ASIC3 acid-evoked currents by retaining the channel intracellularly. May regulate the intracellular trafficking of ADR1B.<ref>PMID:15317815</ref> <ref>PMID:15358863</ref>
	<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 5w72" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5w72" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Postsynaptic density protein 3D structures\|Postsynaptic density protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kudlinzki, D]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Lehner, F]]	+	[[Category: Kudlinzki D]]
-	[[Category: Schwalbe, H]]	+	[[Category: Lehner F]]
-	[[Category: Silvers, R]]	+	[[Category: Schwalbe H]]
-	~~[[Category: Signaling protein~~]]	+	[[Category: Silvers R]]

OCA at 07:41, 24 April 2019

2019-04-24T07:41:33Z

←Older revision		Revision as of 07:41, 24 April 2019
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	==Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography==		==Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography==
-	<StructureSection load='5w72' size='340' side='right' caption='[[5w72]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5w72' size='340' side='right'caption='[[5w72]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w72]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W72 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W72 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w72]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W72 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W72 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZH:AZIDOHOMOALANINE'>AZH</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZH:AZIDOHOMOALANINE'>AZH</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dlg4, Dlgh4, Psd95 ([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=5w72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w72 OCA], [http://pdbe.org/5w72 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w72 RCSB], [http://www.ebi.ac.uk/pdbsum/5w72 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w72 ProSAT]</span></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=5w72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w72 OCA], [http://pdbe.org/5w72 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w72 RCSB], [http://www.ebi.ac.uk/pdbsum/5w72 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w72 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Kudlinzki, D]]		[[Category: Kudlinzki, D]]
	[[Category: Lehner, F]]		[[Category: Lehner, F]]

OCA at 06:58, 13 December 2017

2017-12-13T06:58:38Z

←Older revision		Revision as of 06:58, 13 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5w72 is ~~ON HOLD~~	+	==Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography==
		+	<StructureSection load='5w72' size='340' side='right' caption='[[5w72]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5w72]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W72 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W72 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZH:AZIDOHOMOALANINE'>AZH</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=5w72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w72 OCA], [http://pdbe.org/5w72 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w72 RCSB], [http://www.ebi.ac.uk/pdbsum/5w72 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w72 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DLG4_RAT DLG4_RAT]] Interacts with the cytoplasmic tail of NMDA receptor subunits and shaker-type potassium channels. Required for synaptic plasticity associated with NMDA receptor signaling. Overexpression or depletion of DLG4 changes the ratio of excitatory to inhibitory synapses in hippocampal neurons. May reduce the amplitude of ASIC3 acid-evoked currents by retaining the channel intracellularly. May regulate the intracellular trafficking of ADR1B.<ref>PMID:15317815</ref> <ref>PMID:15358863</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The impact of the incorporation of a non-natural amino acid (NNAA) onto protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro using click-chemistry. Here, we present a structural characterization of the impact of the incorporation of azidohomoalanine (AZH) into the model protein domain PDZ3 using NMR spectroscopy and X-ray crystallography. The structure and dynamics of the apo state of the AZH-modified PDZ3 remains mostly unperturbed. Furthermore, the binding of two PDZ3 binding peptides are found to be unchanged by incorporation of AZH. We mapped the interface of the AZH-modified PDZ3 and an azulene-linked peptide for vibrational energy transfer studies using chemical shift perturbations and NOEs between the unlabelled azulene-linked peptide and the isotopically labelled protein. Co-crystallization and soaking failed for the peptide-bound holo-complex. NMR spectroscopy, however, al-lowed determination of the protein-ligand interface. While the incorpo-ration of AZH was minimally invasive for PDZ3, structural analysis of NNAA-modified proteins by the methodology presented here should be carried out to ensure structural integrity of the studied target.

-	~~Authors: Lehner~~, F., Kudlinzki, D., ~~Schwalbe~~, H., ~~Silvers~~, R.	+	The Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding.,Lehner F, Kudlinzki D, Richter C, Muller-Werkmeister H, Eberl K, Bredenbeck J, Schwalbe H, Silvers R Chembiochem. 2017 Sep 26. doi: 10.1002/cbic.201700437. PMID:28950050<ref>PMID:28950050</ref>

-	~~Description: Impact~~ of ~~IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5w72" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kudlinzki, D]]		[[Category: Kudlinzki, D]]
	[[Category: Lehner, F]]		[[Category: Lehner, F]]
-	[[Category: Silvers, R]]
	[[Category: Schwalbe, H]]		[[Category: Schwalbe, H]]
		+	[[Category: Silvers, R]]
		+	[[Category: Signaling protein]]

OCA: Protected "5w72" [edit=sysop:move=sysop]

2017-09-27T14:30:57Z

Protected "5w72" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:30, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w72 is ON HOLD Authors: Lehner, F., Kudlinzki, D., Schwalbe, H., Silvers, R. Description: Impact of IR active probes on PDZ3 and its ligand bindin...

2017-09-27T14:30:56Z

New page: '''Unreleased structure''' The entry 5w72 is ON HOLD Authors: Lehner, F., Kudlinzki, D., Schwalbe, H., Silvers, R. Description: Impact of IR active probes on PDZ3 and its ligand bindin...

New page

'''Unreleased structure'''

The entry 5w72 is ON HOLD

Authors: Lehner, F., Kudlinzki, D., Schwalbe, H., Silvers, R.

Description: Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography
[[Category: Unreleased Structures]]
[[Category: Kudlinzki, D]]
[[Category: Lehner, F]]
[[Category: Silvers, R]]
[[Category: Schwalbe, H]]