3k66: Difference between revisions

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OCA

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 ==X-ray crystal structure of the E2 domain of C. elegans APL-1==
-<StructureSection load='3k66' size='340' side='right' caption='[[3k66]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='3k66' size='340' side='right'caption='[[3k66]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3k66]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K66 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K66 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3k66]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K66 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1rw6|1rw6]], [[3k6b|3k6b]]</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]] 2.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">apl-1, C42D8.8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=3k66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k66 OCA], [https://pdbe.org/3k66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k66 RCSB], [https://www.ebi.ac.uk/pdbsum/3k66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k66 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=3k66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k66 OCA], [http://pdbe.org/3k66 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k66 RCSB], [http://www.ebi.ac.uk/pdbsum/3k66 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k66 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A4_CAEEL A4_CAEEL]
 == 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/k6/3k66_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k6/3k66_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 19: @@
 </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=3k66 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The amyloid beta-peptide deposit found in the brain tissue of patients with Alzheimer disease is derived from a large heparin-binding protein precursor APP. The biological function of APP and its homologs is not precisely known. Here we report the x-ray structure of the E2 domain of APL-1, an APP homolog in Caenorhabditis elegans, and compare it to the human APP structure. We also describe the structure of APL-1 E2 in complex with sucrose octasulfate, a highly negatively charged disaccharide, which reveals an unexpected binding pocket between the two halves of E2. Based on the crystal structure, we are able to map, using site-directed mutagenesis, a surface groove on E2 to which heparin may bind. Our biochemical data also indicate that the affinity of E2 for heparin is influenced by pH: at pH 5, the binding appears to be much stronger than that at neutral pH. This property is likely caused by histidine residues in the vicinity of the mapped heparin binding site and could be important for the proposed adhesive function of APL-1.
-Structural characterization of the E2 domain of APL-1, a Caenorhabditis elegans homolog of human amyloid precursor protein, and its heparin binding site.,Hoopes JT, Liu X, Xu X, Demeler B, Folta-Stogniew E, Li C, Ha Y J Biol Chem. 2010 Jan 15;285(3):2165-73. Epub 2009 Nov 10. PMID:19906646<ref>PMID:19906646</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3k66" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Caeel]]
+[[Category: Caenorhabditis elegans]]
-[[Category: Ha, Y]]
+[[Category: Large Structures]]
-[[Category: Hoopes, J T]]
+[[Category: Ha Y]]
-[[Category: Alternative splicing]]
+[[Category: Hoopes JT]]
-[[Category: Amyloid]]
-[[Category: Amyloid precursor protein]]
-[[Category: Cell adhesion]]
-[[Category: Developmental protein]]
-[[Category: Differentiation]]
-[[Category: Glycoprotein]]
-[[Category: Heparin binding]]
-[[Category: Membrane]]
-[[Category: Neurogenesis]]
-[[Category: Transmembrane]]
-[[Category: X-ray crystal structure]]