2egd

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[[Image:2egd.png|left|200px]]
 
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==Crystal structure of human S100A13 in the Ca2+-bound state==
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The line below this paragraph, containing "STRUCTURE_2egd", creates the "Structure Box" on the page.
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<StructureSection load='2egd' size='340' side='right'caption='[[2egd]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2egd]] 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=2EGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EGD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_2egd| PDB=2egd | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2egd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2egd OCA], [https://pdbe.org/2egd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2egd RCSB], [https://www.ebi.ac.uk/pdbsum/2egd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2egd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/S10AD_HUMAN S10AD_HUMAN] Plays a role in the export of proteins that lack a signal peptide and are secreted by an alternative pathway. Binds two calcium ions per subunit. Binds one copper ion. Binding of one copper ion does not interfere with calcium binding. Required for the copper-dependent stress-induced export of IL1A and FGF1. The calcium-free protein binds to lipid vesicles containing phosphatidylserine, but not to vesicles containing phosphatidylcholine (By similarity).<ref>PMID:12746488</ref> <ref>PMID:20863990</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eg/2egd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2egd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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S100A13 is a member of the S100 family of EF-hand-containing calcium-binding proteins. S100A13 plays an important role in the secretion of fibroblast growth factor-1 and interleukin 1 alpha, two pro-angiogenic factors released by the nonclassical endoplasmic reticulum/Golgi-independent secretory pathway. The X-ray crystal structure of human S100A13 at pH 7.5 was determined at 1.8 A resolution. The structure was solved by molecular replacement and was refined to a final R factor of 19.0%. The structure revealed that human S100A13 exists as a homodimer with two calcium ions bound to each protomer. The protomer is composed of four alpha-helices (alpha(1)-alpha(4)), which form a pair of EF-hand motifs. Dimerization occurs by hydrophobic interactions between helices alpha(1) and alpha(4) and by intermolecular hydrogen bonds between residues from helix alpha(1) and the residues between alpha(2) and alpha(3) of both chains. Despite the high similarity of the backbone conformation in each protomer, the crystal structures of human S100A13 at pH 7.5 (this study) and at pH 6.0 [Li et al. (2007), Biochem. Biophys. Res. Commun. 356, 616-621] exhibit recognizable differences in the relative orientation ( approximately 2.5 degrees) of the protomers within the dimer and also remarkable differences in the side-chain conformations of several amino-acid residues.
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===Crystal structure of human S100A13 in the Ca2+-bound state===
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Structure of calcium-bound human S100A13 at pH 7.5 at 1.8 A resolution.,Imai FL, Nagata K, Yonezawa N, Nakano M, Tanokura M Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Feb 1;64(Pt, 2):70-6. Epub 2008 Jan 31. PMID:18259052<ref>PMID:18259052</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2egd" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18259052}}, adds the Publication Abstract to the page
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*[[S100 proteins 3D structures|S100 proteins 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18259052 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18259052}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[2egd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EGD OCA].
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==Reference==
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<ref group="xtra">PMID:18259052</ref><ref group="xtra">PMID:17077500</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Imai, F L.]]
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[[Category: Large Structures]]
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[[Category: Nagata, K.]]
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[[Category: Imai FL]]
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[[Category: Nakano, M.]]
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[[Category: Nagata K]]
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[[Category: Tanokura, M.]]
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[[Category: Nakano M]]
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[[Category: Yonezawa, N.]]
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[[Category: Tanokura M]]
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[[Category: Ef-hand]]
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[[Category: Yonezawa N]]
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[[Category: Metal binding protein]]
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Current revision

Crystal structure of human S100A13 in the Ca2+-bound state

PDB ID 2egd

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