3e47: Difference between revisions

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-[[Image:3e47.png|left|200px]]
-{{STRUCTURE_3e47|  PDB=3e47  |  SCENE=  }}
+==Crystal Structure of the Yeast 20S Proteasome in Complex with Homobelactosin C==
+<StructureSection load='3e47' size='340' side='right'caption='[[3e47]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3e47]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fny 2fny]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E47 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ESY:BENZYL+N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N~6~-[(2R,3S,4S)-3-FORMYL-2-HYDROXY-4-METHYLHEXANOYL]-L-LYSINATE'>ESY</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=3e47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e47 OCA], [https://pdbe.org/3e47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e47 RCSB], [https://www.ebi.ac.uk/pdbsum/3e47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e47 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSA2_YEAST PSA2_YEAST] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
+== 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/e4/3e47_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=3e47 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Most class I MHC ligands are generated from the vast majority of cellular proteins by proteolysis within the ubiquitin-proteasome pathway and are presented on the cell surface by MHC class I molecules. Here, we present the crystallographic analysis of yeast 20S proteasome in complex with the inhibitor homobelactosin C. The structure reveals a unique inhibitor-binding mode and provides information about the composition of proteasomal primed substrate-binding sites. IFN-gamma inducible substitution of proteasomal constitutive subunits by immunosubunits modulates characteristics of generated peptides, thus producing fragments with higher preference for binding to MHC class I molecules. The structural data for the proteasome:homobelactosin C complex provide an explanation for involvement of immunosubunits in antigen generation and open perspectives for rational design of ligands, inhibiting exclusively constitutive proteasomes or immunoproteasomes.
-===Crystal Structure of the Yeast 20S Proteasome in Complex with Homobelactosin C===
+Inhibitor-binding mode of homobelactosin C to proteasomes: new insights into class I MHC ligand generation.,Groll M, Larionov OV, Huber R, de Meijere A Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4576-9. Epub 2006 Mar 13. PMID:16537370<ref>PMID:16537370</ref>
-{{ABSTRACT_PUBMED_16537370}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3e47" style="background-color:#fffaf0;"></div>
-[[3e47]] is a 28 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fny 2fny]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E47 OCA].
 ==See Also==
-*[[Proteasome|Proteasome]]
+*[[Proteasome 3D structures|Proteasome 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016537370</ref><references group="xtra"/>
+__TOC__
-[[Category: Proteasome endopeptidase complex]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Groll, M.]]
+[[Category: Groll M]]
-[[Category: Larionov, O V.]]
+[[Category: Larionov OV]]
-[[Category: Meijere, A de.]]
+[[Category: De Meijere A]]
-[[Category: Hydrolase]]
-[[Category: Immunology]]
-[[Category: Inhibitor]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Protease]]
-[[Category: Proteasome]]
-[[Category: Protein degradation]]
-[[Category: Threonine protease]]
-[[Category: Ubiquitin]]
-[[Category: Zymogen]]