2ka9: Difference between revisions

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-{{Seed}}
-[[Image:2ka9.jpg|left|200px]]
-<!--
+==Solution structure of PSD-95 PDZ12 complexed with cypin peptide==
-The line below this paragraph, containing "STRUCTURE_2ka9", creates the "Structure Box" on the page.
+<StructureSection load='2ka9' size='340' side='right'caption='[[2ka9]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ka9]] is a 3 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=2KA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KA9 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ka9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ka9 OCA], [https://pdbe.org/2ka9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ka9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ka9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ka9 ProSAT]</span></td></tr>
-{{STRUCTURE_2ka9|  PDB=2ka9  |  SCENE=  }}
+</table>
+== Function ==
+[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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ka/2ka9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ka9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The two N-terminal PDZ domains of postsynaptic density protein-95 (PDS-95 PDZ1 and PDZ2) are closely connected in tandem by a conserved peptide linker of five amino acids. The interdomain orientation between PDZ1 and PDZ2 of the ligand-free PDZ12 tandem is restrained, and this conformational arrangement facilitates the synergistic binding of PDZ12 to multimeric targets. (1) The interdomain orientation of the target-bound state of PDZ12 is not known. Here, we have solved the structure of PDZ12 in complex with its binding domain from cypin. Both chemical shift data and residual dipolar coupling measurements showed that the restrained interdomain orientation disappeared upon cypin peptide binding. NMR-based relaxation experiments revealed slow interdomain motions in the PDZ12/cypin peptide complex. Molecular dynamics simulations also showed that the PDZ12/cypin complex has larger conformational flexibility than the ligand-free PDZ12. This dramatic change of protein dynamics provides extra conformational entropy upon ligand binding, thus enhancing the ligand binding affinity of the PDZ12 tandem. Modulation of ligand binding affinity through concerted interdomain structural and dynamic rearrangements may represent a general property of multidomain scaffold proteins.
-===Solution structure of PSD-95 PDZ12 complexed with cypin peptide===
+Creating conformational entropy by increasing interdomain mobility in ligand binding regulation: a revisit to N-terminal tandem PDZ domains of PSD-95.,Wang W, Weng J, Zhang X, Liu M, Zhang M J Am Chem Soc. 2009 Jan 21;131(2):787-96. PMID:19072119<ref>PMID:19072119</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ka9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19072119}}, adds the Publication Abstract to the page
+*[[Postsynaptic density protein 3D structures|Postsynaptic density protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19072119 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19072119}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-KA9 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KA9 OCA].
-==Reference==
-<ref group="xtra">PMID:19072119</ref><references group="xtra"/>
 [[Category: Rattus norvegicus]]
-[[Category: Liu, M L.]]
+[[Category: Liu ML]]
-[[Category: Wang, W N.]]
+[[Category: Wang WN]]
-[[Category: Weng, J W.]]
+[[Category: Weng JW]]
-[[Category: Zhang, M J.]]
+[[Category: Zhang MJ]]
-[[Category: Zhang, X.]]
+[[Category: Zhang X]]
-[[Category: Alternative splicing]]
-[[Category: Cell adhesion]]
-[[Category: Cell junction]]
-[[Category: Cell membrane]]
-[[Category: Lipoprotein]]
-[[Category: Membrane]]
-[[Category: Palmitate]]
-[[Category: Pdz-cypin peptide complex]]
-[[Category: Phosphoprotein]]
-[[Category: Postsynaptic cell membrane]]
-[[Category: Sh3 domain]]
-[[Category: Synapse]]
-[[Category: Tandem pdz domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 09:17:50 2009''