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Dong"],"technology_type":["Mass Spectrometry","Chemical cross-linking coupled with mass spectrometry proteomics"],"software":["Not available"],"submitter_keywords":["Ubiquitin","26s proteasome","Ubiquitin receptors"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075114"],"sample_protocol":["1.5 μM yeast 26S proteasome was crosslinked to 1 μM Ub(L73BPA) in 40 μL by incubation on ice under UV light (365 nm) for 30 minutes. The sample was diluted to 1 mL in Denaturing Buffer (50 mM HEPES pH 7.6, 20 mM imidazole, 6 M guanidine hydrochloride) and incubated at room temperature for 15 minutes. The sample was loaded onto a 1 mL HiTrap column (Cytiva) equilibrated with Denaturing Buffer, washed twice with 5 mL Denaturing Buffer, and eluted with 7 mL of 50 mM HEPES pH 7.6, 250 mM imidazole, 6 M guanidine hydrochloride. The sample was concentrated in a 3K cutoff concentrator and buffer exchanged into 50 mM ammonium bicarbonate pH 8, before reducing the volume to 50 μL. The sample volume was brought to 60 μL with 50 mM ammonium bicarbonate pH 8 and 25% acetonitrile. TCEP was added to a final concentration of 5 mM, and the sample was incubated at room temperature for 20 minutes. Iodoacetamide was added to a final concentration of 10 mM, and the sample was incubated at room temperature in the dark for 20 minutes. CaCl2 was added to a final concentration of 1 mM, and the sample was incubated overnight at 37 °C with at least 1 μg trypsin. The sample was acidified with formic acid to 5%, diluted, and reduced in volume to 10 μL in a Speedvac.In-gel trypsin-digested peptides from crosslinked 26S proteasome samples were filtered with a 0.22 μm centrifugal filter (Millipore UFC30GVNB) and manually loaded on an in-house prepared fused silica capillary column (250 μm X 35cm) with Kasil outlet end. The column was packed with ReproSil pHoenix C18-3.0 μm high PH resin (Dr. Maisch GmbH). Peptides were eluted at a flow rate of 2 μL/min using a linear gradient of 2–40% buffer B in 140 min (buffer A: 0.1% triethylamine (TEA) pH 10.0, 5% acetonitrile in water; buffer B: 0.1% TEA pH 10.0, 95% acetonitrile in water) with an Agilent 1200 nanoflow LC. Samples were collected every 3 minutes during the gradient using a fraction collector (Biorad 2110). The 60 fractions were concatenated to 8 fractions and acidified with formic acid to pH 2.0, before reducing their volume to 10 μL in a Speedvac.Trypsin-digested peptides were analyzed by online capillary nanoLC-MS/MS using a 25 cm reversed phase column and a 10 cm pre-column fabricated in-house (75 µm inner diameter, packed with ReproSil-Gold C18-1.9 μm resin (Dr. Maisch GmbH)) that was equipped with a laser-pulled nano-electrospray emitter tip. The pre-column used 3.0 μm packing (Dr. Maisch GmbH). Peptides were eluted at a flow rate of 300 nL/min using a linear gradient of 2–40% buffer B in 140 min (buffer A: 0.05% formic acid, 5% acetonitrile in water; buffer B: 0.05% formic acid, 95% acetonitrile in water) in an Thermo Fisher Easy-nLC1200 nanoLC system. Peptides were ionized using a FLEX ion source (Thermo Fisher Scientific) using electrospray ionization into an Fusion Lumos Tribrid Orbitrap Mass Spectrometer (Thermo Fisher Scientific). Data were acquired in Orbi-trap mode. Instrument method parameters were as follows: MS1 resolution, 120,000 at 200 m/z; scan range, 350−1600 m/z. The top 20 most-abundant ions were subjected to collision-induced dissociation with a normalized collision energy of 35%, activation q 0.25, and precursor isolation width 2 m/z. Dynamic exclusion was enabled with a repeat count of 1, a repeat duration of 30 seconds, and an exclusion duration of 20 seconds."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Crosslinked peptides were identified using the pLink software 31. MGF files exported from PEAKS (Bioinformatics Solutions Inc.) were searched with the following parameters: crosslinker set as BPA, enzyme type was set to nonspecific, up to 3 missed cleavages, peptide mass 600 - 10000 Da, peptide length 4 – 100 residues, precursor tolerance set to 10 ppm, fragment tolerance set to 10 ppm, fixed carbaminomethyl C modification, variable oxidation M modification, with a reference database containing the Ub(BPA) sequence and the sequence of 1-2 proteasome subunits. Each subunit was included in 4 different reference databases, once as the only sequence other than Ub(BPA). Crosslinked peptides that were identified in 75-100% of searches for that subunit were considered true positive hits. Crosslinked peptides identified in 50% or fewer of searches were considered false positives. Spectra corresponding to the crosslinked peptides were analyzed in pLabel and plotted in GraphPad Prism."],"omics_type":["Proteomics"],"labhead":["Andreas Martin"],"instrument_platform":[""],"labhead_affiliation":["Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720 USA California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720 Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720 USA"],"submission_type":["PARTIAL"],"species":["Saccharomyces Cerevisiae (baker's Yeast)"],"submitter_mail":["k77dong@berkeley.edu"],"publication":["42031168 MacRae NS, Dong KC, Harimoto H, Martin A. Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry. J Biol Chem. 2026 302(6):111481 10.1016/j.jbc.2026.111481"],"submitter_affiliation":["Howard Hughes Medical Institute/ UC Berkeley"],"submitter_country":["United States"],"pubmed_abstract":["The 26S proteasome is the endpoint of the ubiquitin-proteasome system, an essential pathway for maintaining cellular homeostasis through targeted degradation of misfolded, damaged, and obsolete proteins. Substrates labeled with ubiquitin are directed to the 26S proteasome by binding to one or more ubiquitin receptors. However, ubiquitin-dependent degradation occurs even when the canonical receptor sites are mutated, suggesting the presence of additional, unidentified binding sites. Here we created photo-crosslinkable probes for ubiquitin interactions by incorporating the unnatural amino acid p-benzoyl-L-phenylalanine into ubiquitin. We show that these probes can be used to measure apparent affinities for known receptors and to reveal novel ubiquitin-binding sites on the yeast 26S proteasome. Through photo-crosslinking mass-spectrometry experiments, we identified a groove on the top of the proteasome, formed by Rpn2, Rpn9, Rpn10, and Rpn12, that serves as an additional tubiquitin-binding interface. Our photo-crosslinkable probes thus serve as versatile tools for the characterization of ubiquitin-protein interactions and the identification of ubiquitin-binding domains."],"pubmed_title":["Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry."],"pubmed_authors":["MacRae Nicole S NS, Dong Ken C KC, Harimoto Hiromitsu H, Martin Andreas A"],"additional_accession":[]},"is_claimable":false,"name":"Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry","description":"The 26S proteasome is the endpoint of the ubiquitin-proteasome system, an essential pathway for maintaining cellular homeostasis through targeted degradation of misfolded, damaged, and obsolete proteins. Substrates labeled with ubiquitin are directed to the 26S proteasome by binding to one or more ubiquitin receptors. However, ubiquitin-dependent degradation occurs even when the canonical receptor sites are mutated, suggesting the presence of additional, unidentified binding sites. Here we created photo-crosslinkable probes for ubiquitin interactions by incorporating the unnatural amino acid p-benzoyl-L-phenylalanine into ubiquitin. We show that these probes can be used to measure apparent affinities for known receptors and to reveal novel ubiquitin-binding sites on the yeast 26S proteasome. Through photo-crosslinking mass-spectrometry experiments we identified a groove on the top of the proteasome, formed by Rpn2, Rpn9, Rpn10, and Rpn12, that serves as an additional ubiquitin-binding interface. Our photo-crosslinkable probes thus serve as versatile tools for the characterization of ubiquitin-protein interactions and the identification of ubiquitin-binding domains.","dates":{"publication":"2026-06-08","submission":"2026-03-03"},"accession":"PXD075114","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:260201","NEWT:35554","NCBITaxon:12939","NEWT:32046","NEWT:544496","NEWT:59529","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:10245","NEWT:55153","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:351581","NEWT:43186","NEWT:428146","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:661410","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:1401257","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:641809","NEWT:27933","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:111225","NEWT:7719","NEWT:7959","NEWT:2261","NEWT:868565","NEWT:94323","NEWT:31156","NEWT:3112","NEWT:79329","NEWT:4442","NEWT:192875","NEWT:1214915","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:284218","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:160621","NEWT:212790","NEWT:931281","NEWT:4432","NEWT:5762","NEWT:5763","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:2246","NEWT:2652724","NEWT:1912919","NEWT:5757","NEWT:68415","NCBITaxon:4563","NEWT:5755","NEWT:44688","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:347256","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:1367269","NEWT:145458","NEWT:633149","NEWT:1149786","NEWT:10239","NEWT:68895","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5744","NEWT:72901","NEWT:213863","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1235816","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:1772","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:11988","NEWT:284812","NEWT:8175","NEWT:400667","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:459758","NEWT:3702","NEWT:1245466","NEWT:243277","NEWT:1246791","NEWT:7067","NEWT:118694","NEWT:586722","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:274","NEWT:7070","NCBITaxon:287","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1303443","NEWT:9483","NEWT:333760","NEWT:34607","NEWT:56636","NEWT:1513458","NEWT:1233681","NEWT:2709072","NCBITaxon:40559","NEWT:506599","NEWT:2853422","NEWT:81077","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:65349","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NEWT:34613","NCBITaxon:4932","NEWT:109760","NEWT:29031","NEWT:943274","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:886559","NEWT:3750","NEWT:55521","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:1130798","NEWT:55529","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1116234","NEWT:561007","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:203696","NEWT:472","NEWT:352472","NEWT:97441","NEWT:1071661","NEWT:1202531","NEWT:1202532","NEWT:360094","NEWT:1408223","NEWT:470","NEWT:1408224","NEWT:41364","NEWT:5911","NEWT:1313","NEWT:1218097","NEWT:1080348","NCBITaxon:50557","NEWT:1314","NEWT:39251","NEWT:39491","NEWT:212142","NCBITaxon:5811","NEWT:29491","NEWT:101841","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:688333","NEWT:215402","NCBITaxon:548681","NEWT:318586","NCBITaxon:5820","NEWT:1547","NEWT:272634","NEWT:198107","NEWT:9031","NEWT:27292","NEWT:1872122","NEWT:1308","NEWT:7091","NEWT:1034015","NEWT:760568","NEWT:141262","NEWT:108931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