2fcq: Difference between revisions

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OCA

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-[[Image:2fcq.gif|left|200px]]<br />
-<applet load="2fcq" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2fcq, resolution 3.30&Aring;" />
-'''X-ray Crystal Structure of a Chemically Synthesized Ubiquitin with a Cubic Space Group'''<br />
-==Overview==
+==X-ray Crystal Structure of a Chemically Synthesized Ubiquitin with a Cubic Space Group==
-The alpha-helix is a fundamental protein structural motif and is, frequently terminated by a glycine residue. Explanations for the, predominance of glycine at the C-cap terminal portions of alpha-helices, have invoked uniquely favorable energetics of this residue in a, left-handed conformation or enhanced solvation of the peptide backbone, because of the absence of a side chain. Attempts to quantify the, contributions of these two effects have been made previously, but the, issue remains unresolved. Here we have used chemical protein synthesis to, dissect the energetic basis of alpha-helix termination by comparing a, series of ubiquitin variants containing an L-amino acid or the, corresponding D-amino acid at the C-cap Gly35 position. D-Amino acids can, adopt a left-handed conformation without energetic penalty, so the, contributions of conformational strain and backbone solvation can thus be, separated. Analysis of the thermodynamic data revealed that the preference, for glycine at the C' position of a helix is predominantly a, conformational effect.
+<StructureSection load='2fcq' size='340' side='right'caption='[[2fcq]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2fcq]] 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=2FCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FCQ 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]] 3.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</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=2fcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcq OCA], [https://pdbe.org/2fcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fcq RCSB], [https://www.ebi.ac.uk/pdbsum/2fcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9PST8_CHICK Q9PST8_CHICK]
+== 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/fc/2fcq_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=2fcq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The alpha-helix is a fundamental protein structural motif and is frequently terminated by a glycine residue. Explanations for the predominance of glycine at the C-cap terminal portions of alpha-helices have invoked uniquely favorable energetics of this residue in a left-handed conformation or enhanced solvation of the peptide backbone because of the absence of a side chain. Attempts to quantify the contributions of these two effects have been made previously, but the issue remains unresolved. Here we have used chemical protein synthesis to dissect the energetic basis of alpha-helix termination by comparing a series of ubiquitin variants containing an L-amino acid or the corresponding D-amino acid at the C-cap Gly35 position. D-Amino acids can adopt a left-handed conformation without energetic penalty, so the contributions of conformational strain and backbone solvation can thus be separated. Analysis of the thermodynamic data revealed that the preference for glycine at the C' position of a helix is predominantly a conformational effect.
-==About this Structure==
+Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.,Bang D, Gribenko AV, Tereshko V, Kossiakoff AA, Kent SB, Makhatadze GI Nat Chem Biol. 2006 Mar;2(3):139-43. Epub 2006 Jan 30. PMID:16446709<ref>PMID:16446709</ref>
-FCQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with CD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FCQ OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis., Bang D, Gribenko AV, Tereshko V, Kossiakoff AA, Kent SB, Makhatadze GI, Nat Chem Biol. 2006 Mar;2(3):139-43. Epub 2006 Jan 30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16446709 16446709]
+</div>
-[[Category: Single protein]]
+<div class="pdbe-citations 2fcq" style="background-color:#fffaf0;"></div>
-[[Category: Bang, D.]]
-[[Category: Gribenko, A.V.]]
-[[Category: Kent, S.B.]]
-[[Category: Kossiakoff, A.A.]]
-[[Category: Makhatadze, G.I.]]
-[[Category: Tereshko, V.]]
-[[Category: CD]]
-[[Category: ubiquitin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 22:03:25 2007''
+==See Also==
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Bang D]]
+[[Category: Gribenko AV]]
+[[Category: Kent SB]]
+[[Category: Kossiakoff AA]]
+[[Category: Makhatadze GI]]
+[[Category: Tereshko V]]