2nbw: Difference between revisions

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 ==Solution structure of the Rpn1 T1 site with the Rad23 UBL domain==
-<StructureSection load='2nbw' size='340' side='right'caption='[[2nbw]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='2nbw' size='340' side='right'caption='[[2nbw]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nbw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NBW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nbw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NBW FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nbu|2nbu]], [[2nbv|2nbv]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPN1, HRD2, NAS1, RPD1, YHR027C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RAD23, YEL037C, SYGP-ORF29 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=2nbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nbw OCA], [https://pdbe.org/2nbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nbw RCSB], [https://www.ebi.ac.uk/pdbsum/2nbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nbw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RPN1_YEAST RPN1_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/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.
+[https://www.uniprot.org/uniprot/RPN1_YEAST RPN1_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>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Three receptors (Rpn1/S2/PSMD2, Rpn10/S5a, Rpn13/Adrm1) in the proteasome bind substrates by interacting with conjugated ubiquitin chains and/or shuttle factors (Rad23/HR23, Dsk2/PLIC/ubiquilin, Ddi1) that carry ubiquitinated substrates to proteasomes. We solved the structure of two such receptors with their preferred shuttle factor, namely hRpn13Pru:hPLIC2UBL and scRpn1 T1:scRad23UBL. We find that ubiquitin folds in Rad23 and Dsk2 are fine-tuned by residue substitutions to achieve high affinity for Rpn1 and Rpn13, respectively. A single substitution in hPLIC2 yields enhanced interactions with the Rpn13 ubiquitin contact surface and sterically blocks hRpn13 binding to its preferred ubiquitin chain type, K48-linked chains. Rpn1 T1 binds two ubiquitins in tandem and we find that Rad23 binds exclusively to the higher-affinity Helix28/Helix30 site. Rad23 contacts at Helix28/Helix30 are optimized compared to ubiquitin by multiple conservative amino acid substitutions. Thus, shuttle factors deliver substrates to proteasomes through fine-tuned ubiquitin-like surfaces.
-Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.,Chen X, Randles L, Shi K, Tarasov SG, Aihara H, Walters KJ Structure. 2016 Jul 6. pii: S0969-2126(16)30125-3. doi:, 10.1016/j.str.2016.05.018. PMID:27396824<ref>PMID:27396824</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2nbw" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[UV excision repair protein|UV excision repair protein]]
+*[[UV excision repair protein 3D structures|UV excision repair protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Chen, X]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Walters, K J]]
+[[Category: Chen X]]
-[[Category: Protein binding]]
+[[Category: Walters KJ]]