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| | <SX load='3jck' size='340' side='right' viewer='molstar' caption='[[3jck]], [[Resolution|resolution]] 3.50Å' scene=''> | | <SX load='3jck' size='340' side='right' viewer='molstar' caption='[[3jck]], [[Resolution|resolution]] 3.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3jck]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JCK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3jck]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JCK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.5Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPN3, SUN2, YER021W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN5, NAS5, YDL147W, D1572 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN6, NAS4, YDL097C, D2381 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN7, YPR108W, P8283.8 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN8, YOR261C, O5360 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN9, NAS7, YDR427W, D9461.14 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN11, MPR1, YFR004W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN12, NIN1, YFR052W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), SEM1, DSH1, YDR363W-A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span></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=3jck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jck OCA], [https://pdbe.org/3jck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jck RCSB], [https://www.ebi.ac.uk/pdbsum/3jck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jck ProSAT]</span></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=3jck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jck OCA], [https://pdbe.org/3jck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jck RCSB], [https://www.ebi.ac.uk/pdbsum/3jck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jck ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RPN9_YEAST RPN9_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [[https://www.uniprot.org/uniprot/RPN6_YEAST RPN6_YEAST]] Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. In the complex, RPN6 is required for proteasome assembly.<ref>PMID:9426256</ref> <ref>PMID:12486135</ref> <ref>PMID:15611133</ref> [[https://www.uniprot.org/uniprot/RPN11_YEAST RPN11_YEAST]] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:21075847</ref> [[https://www.uniprot.org/uniprot/SEM1_YEAST SEM1_YEAST]] Versatile protein that might stabilize multiple protein complexes involved in diverse pathways. Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis. Associates also with the TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation.<ref>PMID:19289793</ref> <ref>PMID:15117943</ref> [[https://www.uniprot.org/uniprot/RPN5_YEAST RPN5_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9426256</ref> [[https://www.uniprot.org/uniprot/RPN12_YEAST RPN12_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase. [[https://www.uniprot.org/uniprot/RPN3_YEAST RPN3_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [[https://www.uniprot.org/uniprot/RPN7_YEAST RPN7_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins (By similarity). [[https://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref>
| + | [https://www.uniprot.org/uniprot/RPN3_YEAST RPN3_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal of ubiquitin chains from targeted substrates at the proteasome is a prerequisite for substrate processing and is accomplished by Rpn11, a deubiquitinase within the 'lid' sub-complex. Prior to the lid's incorporation into the proteasome, Rpn11 deubiquitinase activity is inhibited to prevent unwarranted deubiquitination of polyubiquitinated proteins. Here we present the atomic model of the isolated lid sub-complex, as determined by cryo-electron microscopy at 3.5 A resolution, revealing how Rpn11 is inhibited through its interaction with a neighboring lid subunit, Rpn5. Through mutagenesis of specific residues, we describe the network of interactions that are required to stabilize this inhibited state. These results provide significant insight into the intricate mechanisms of proteasome assembly, outlining the substantial conformational rearrangements that occur during incorporation of the lid into the 26S holoenzyme, which ultimately activates the deubiquitinase for substrate degradation.
| + | |
| - | | + | |
| - | Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition.,Dambacher CM, Worden EJ, Herzik MA, Martin A, Lander GC Elife. 2016 Jan 8;5. pii: e13027. doi: 10.7554/eLife.13027. PMID:26744777<ref>PMID:26744777</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3jck" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Baker's yeast]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ubiquitinyl hydrolase 1]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Dambacher, C M]] | + | [[Category: Dambacher CM]] |
| - | [[Category: Herzik, M A]] | + | [[Category: Herzik Jr MA]] |
| - | [[Category: Lander, G C]] | + | [[Category: Lander GC]] |
| - | [[Category: Martin, A]] | + | [[Category: Martin A]] |
| - | [[Category: Worden, E J]] | + | [[Category: Worden EJ]] |
| - | [[Category: Deubiquitinase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Proteasome]]
| + | |
| - | [[Category: Protein homeostasis]]
| + | |
| - | [[Category: Rpn11]]
| + | |
