1hd3: Difference between revisions

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-[[Image:1hd3.png|left|200px]]
-<!--
+==A-SPECTRIN SH3 DOMAIN F52Y MUTANT==
-The line below this paragraph, containing "STRUCTURE_1hd3", creates the "Structure Box" on the page.
+<StructureSection load='1hd3' size='340' side='right'caption='[[1hd3]], [[Resolution|resolution]] 1.98&Aring;' 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'>[[1hd3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HD3 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">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1hd3|  PDB=1hd3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hd3 OCA], [https://pdbe.org/1hd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1hd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hd3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPTN1_CHICK SPTN1_CHICK] Morphologically, spectrin-like proteins appear to be related to spectrin, showing a flexible rod-like structure. They can bind actin but seem to differ in their calmodulin-binding activity. In nonerythroid tissues, spectrins, in association with some other proteins, may play an important role in membrane organization.
+== 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/hd/1hd3_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=1hd3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Here we present a method for determining the inference of non-native conformations in the folding of a small domain, alpha-spectrin Src homology 3 domain. This method relies on the preservation of all native interactions after Tyr/Phe exchanges in solvent-exposed, contact-free positions. Minor changes in solvent exposure and free energy of the denatured ensemble are in agreement with the reverse hydrophobic effect, as the Tyr/Phe mutations slightly change the polypeptide hydrophilic/hydrophobic balance. Interestingly, more important Gibbs energy variations are observed in the transition state ensemble (TSE). Considering the small changes induced by the H/OH replacements, the observed energy variations in the TSE are rather notable, but of a magnitude that would remain undetected under regular mutations that alter the folded structure free energy. Hydrophobic residues outside of the folding nucleus contribute to the stability of the TSE in an unspecific nonlinear manner, producing a significant acceleration of both unfolding and refolding rates, with little effect on stability. These results suggest that sectors of the protein transiently reside in non-native areas of the landscape during folding, with implications in the reading of phi values from protein engineering experiments. Contrary to previous proposals, the principle that emerges is that non-native contacts, or conformations, could be beneficial in evolution and design of some fast folding proteins.
-===A-SPECTRIN SH3 DOMAIN F52Y MUTANT===
+Unspecific hydrophobic stabilization of folding transition states.,Viguera AR, Vega C, Serrano L Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5349-54. PMID:11959988<ref>PMID:11959988</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_11959988}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1hd3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11959988 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_11959988}}
-==About this Structure==
-[[1hd3]] is a 1 chain structure of [[Spectrin]] with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HD3 OCA].
 ==See Also==
-*[[Spectrin]]
+*[[Spectrin 3D structures|Spectrin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:11959988</ref><ref group="xtra">PMID:1279434</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Serrano, L.]]
+[[Category: Large Structures]]
-[[Category: Vega, M C.]]
+[[Category: Serrano L]]
-[[Category: Viguera, A R.]]
+[[Category: Vega MC]]
-[[Category: Actin-binding]]
+[[Category: Viguera AR]]
-[[Category: Calmodulin-binding]]
-[[Category: Cytoskeleton]]
-[[Category: Sh3-domain]]