2hkd: Difference between revisions

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-[[Image:2hkd.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2hkd", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2hkd|  PDB=2hkd  |  SCENE=  }}
-'''The crystal structure of engineered OSPA'''
+==The crystal structure of engineered OSPA==
+<StructureSection load='2hkd' size='340' side='right'caption='[[2hkd]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2hkd]] 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=2HKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HKD 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]] 1.6&#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=2hkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hkd OCA], [https://pdbe.org/2hkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hkd RCSB], [https://www.ebi.ac.uk/pdbsum/2hkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hkd 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/hk/2hkd_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=2hkd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Although the beta-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the beta-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble protein. We tested this strategy by using Borrelia outer surface protein (OspA) whose single-layer beta-sheet located between two globular domains consists of two beta-hairpin units and thus can be considered as a prototype of self-assembly. We constructed self-assembly mimics of different sizes and determined their atomic structures using x-ray crystallography and NMR spectroscopy. Highly regular beta-sheet geometries were maintained in these structures, and peptide units had a nearly identical conformation, supporting the concept that a peptide in the regular beta-geometry is primed for self-assembly. However, we found small but significant differences in the relative orientation between adjacent peptide units in terms of beta-sheet twist and bend, suggesting their inherent flexibility. Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies.
-==Overview==
+Atomic structures of peptide self-assembly mimics.,Makabe K, McElheny D, Tereshko V, Hilyard A, Gawlak G, Yan S, Koide A, Koide S Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17753-8. Epub 2006 Nov 8. PMID:17093048<ref>PMID:17093048</ref>
-Although the beta-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the beta-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble protein. We tested this strategy by using Borrelia outer surface protein (OspA) whose single-layer beta-sheet located between two globular domains consists of two beta-hairpin units and thus can be considered as a prototype of self-assembly. We constructed self-assembly mimics of different sizes and determined their atomic structures using x-ray crystallography and NMR spectroscopy. Highly regular beta-sheet geometries were maintained in these structures, and peptide units had a nearly identical conformation, supporting the concept that a peptide in the regular beta-geometry is primed for self-assembly. However, we found small but significant differences in the relative orientation between adjacent peptide units in terms of beta-sheet twist and bend, suggesting their inherent flexibility. Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-HKD is a [[Single protein]] structure of 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=2HKD OCA].
+</div>
+<div class="pdbe-citations 2hkd" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Atomic structures of peptide self-assembly mimics., Makabe K, McElheny D, Tereshko V, Hilyard A, Gawlak G, Yan S, Koide A, Koide S, Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17753-8. Epub 2006 Nov 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17093048 17093048]
+*[[Outer surface protein|Outer surface protein]]
-[[Category: Borrelia burgdorferi]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Koide, S.]]
+__TOC__
-[[Category: Makabe, K.]]
+</StructureSection>
-[[Category: Terechko, V.]]
+[[Category: Borreliella burgdorferi]]
-[[Category: Beta sheet]]
+[[Category: Large Structures]]
-[[Category: Engineered protein]]
+[[Category: Koide S]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:23:40 2008''
+[[Category: Makabe K]]
+[[Category: Terechko V]]