4rca: Difference between revisions

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 ==Crystal structure of human PTPdelta and human Slitrk1 complex==
-<StructureSection load='4rca' size='340' side='right' caption='[[4rca]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
+<StructureSection load='4rca' size='340' side='right'caption='[[4rca]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rca]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RCA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rca]] 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=4RCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RCA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.9908&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4rca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rca RCSB], [http://www.ebi.ac.uk/pdbsum/4rca PDBsum]</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=4rca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rca OCA], [https://pdbe.org/4rca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rca RCSB], [https://www.ebi.ac.uk/pdbsum/4rca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rca ProSAT]</span></td></tr>
 </table>
-== Disease ==
-[[http://www.uniprot.org/uniprot/SLIK1_HUMAN SLIK1_HUMAN]] Tourette syndrome. The disease may be caused by mutations affecting the gene represented in this entry.  The disease may be caused by mutations affecting the gene represented in this entry.
 == Function ==
-[[http://www.uniprot.org/uniprot/SLIK1_HUMAN SLIK1_HUMAN]] Enhances neuronal dendrite outgrowth.<ref>PMID:16224024</ref>
+[https://www.uniprot.org/uniprot/PTPRD_HUMAN PTPRD_HUMAN]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Synaptic adhesion molecules orchestrate synaptogenesis. The presynaptic leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) regulate synapse development by interacting with postsynaptic Slit- and Trk-like family proteins (Slitrks), which harbour two extracellular leucine-rich repeats (LRR1 and LRR2). Here we identify the minimal regions of the LAR-RPTPs and Slitrks, LAR-RPTPs Ig1-3 and Slitrks LRR1, for their interaction and synaptogenic function. Subsequent crystallographic and structure-guided functional analyses reveal that the splicing inserts in LAR-RPTPs are key molecular determinants for Slitrk binding and synapse formation. Moreover, structural comparison of the two Slitrk1 LRRs reveal that unique properties on the concave surface of Slitrk1 LRR1 render its specific binding to LAR-RPTPs. Finally, we demonstrate that lateral interactions between adjacent trans-synaptic LAR-RPTPs/Slitrks complexes observed in crystal lattices are critical for Slitrk1-induced lateral assembly and synaptogenic activity. Thus, we propose a model in which Slitrks mediate synaptogenic functions through direct binding to LAR-RPTPs and the subsequent lateral assembly of LAR-RPTPs/Slitrks complexes.
+Structural basis for LAR-RPTP/Slitrk complex-mediated synaptic adhesion.,Um JW, Kim KH, Park BS, Choi Y, Kim D, Kim CY, Kim SJ, Kim M, Ko JS, Lee SG, Choii G, Nam J, Heo WD, Kim E, Lee JO, Ko J, Kim HM Nat Commun. 2014 Nov 14;5:5423. doi: 10.1038/ncomms6423. PMID:25394468<ref>PMID:25394468</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4rca" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Tyrosine phosphatase 3D structures|Tyrosine phosphatase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Protein-tyrosine-phosphatase]]
+[[Category: Homo sapiens]]
-[[Category: Kim, D]]
+[[Category: Large Structures]]
-[[Category: Kim, H M]]
+[[Category: Kim D]]
-[[Category: Lee, S G]]
+[[Category: Kim HM]]
-[[Category: Park, B S]]
+[[Category: Lee SG]]
-[[Category: Ig-like domain]]
+[[Category: Park BS]]
-[[Category: Leucine rich-repeat]]
-[[Category: Signaling protein]]
-[[Category: Synaptic adhesion]]