3ec5: Difference between revisions

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-[[Image:3ec5.png|left|200px]]
-{{STRUCTURE_3ec5|  PDB=3ec5  |  SCENE=  }}
+==The crystal structure of Thioflavin-T (ThT) binding OspA mutant==
+<StructureSection load='3ec5' size='340' side='right'caption='[[3ec5]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ec5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Borreliella_burgdorferi Borreliella burgdorferi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EC5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></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=3ec5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ec5 OCA], [https://pdbe.org/3ec5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ec5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ec5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ec5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/D0VWU8_BORBG D0VWU8_BORBG]
+== 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/ec/3ec5_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=3ec5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A number of small organic molecules have been developed that bind to amyloid fibrils, a subset of which also inhibit fibrillization. Among these, the benzothiol dye Thioflavin-T (ThT) has been used for decades in the diagnosis of protein-misfolding diseases and in kinetic studies of self-assembly (fibrillization). Despite its importance, efforts to characterize the ThT-binding mechanism at the atomic level have been hampered by the inherent insolubility and heterogeneity of peptide self-assemblies. To overcome these challenges, we have developed a minimalist approach to designing a ThT-binding site in a "peptide self-assembly mimic" (PSAM) scaffold. PSAMs are engineered water-soluble proteins that mimic a segment of beta-rich peptide self-assembly, and they are amenable to standard biophysical techniques and systematic mutagenesis. The PSAM beta-sheet contains rows of repetitive amino acid patterns running perpendicular to the strands (cross-strand ladders) that represent a ubiquitous structural feature of fibril-like surfaces. We successfully designed a ThT-binding site that recapitulates the hallmarks of ThT-fibril interactions by constructing a cross-strand ladder consisting of contiguous tyrosines. The X-ray crystal structures suggest that ThT interacts with the beta-sheet by docking onto surfaces formed by a single tyrosine ladder, rather than in the space between adjacent ladders. Systematic mutagenesis further demonstrated that tyrosine surfaces across four or more beta-strands formed the minimal binding site for ThT. Our work thus provides structural insights into how this widely used dye recognizes a prominent subset of peptide self-assemblies, and proposes a strategy to elucidate the mechanisms of fibril-ligand interactions.
-===The crystal structure of Thioflavin-T (ThT) binding OspA mutant===
+Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies.,Biancalana M, Makabe K, Koide A, Koide S J Mol Biol. 2009 Jan 30;385(4):1052-63. Epub 2008 Nov 14. PMID:19038267<ref>PMID:19038267</ref>
-{{ABSTRACT_PUBMED_19038267}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ec5" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3ec5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Borrelia_burgdorferi Borrelia burgdorferi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EC5 OCA].
+*[[Outer surface protein|Outer surface protein]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019038267</ref><references group="xtra"/>
+__TOC__
-[[Category: Borrelia burgdorferi]]
+</StructureSection>
-[[Category: Biancalana, M.]]
+[[Category: Borreliella burgdorferi]]
-[[Category: Koide, A.]]
+[[Category: Large Structures]]
-[[Category: Koide, S.]]
+[[Category: Biancalana M]]
-[[Category: Makabe, K.]]
+[[Category: Koide A]]
-[[Category: Membrane protein]]
+[[Category: Koide S]]
-[[Category: Single-layer beta-sheet]]
+[[Category: Makabe K]]