{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/20260203_111524_PA200-Review_NativePeptides_ABR_03022026_PEPReport.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/20260203_111524_PA200-Review_NativePeptides_ABR_03022026_PROTReport.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/SDRF.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/checksum.txt"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/UniProtKB_Human_SWPR-contFK_20250731.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_alone_rep1_1716.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_PA200_rep4_1709.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_PA200_rep2_1702.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_control_rep3_1723.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_PA200_rep3_1703.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_control_rep4_1724.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_alone_rep5_1715.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_alone_rep3_1718.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_PA200_rep2_1707.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_control_rep2_1722.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_PA200_rep4_1704.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_PA200_rep5_1710.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_alone_rep4_1714.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_PA200_rep3_1708.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_alone_rep2_1717.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_PA200_rep5_1705.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_alone_rep5_1720.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_alone_rep3_1713.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_alone_rep2_1712.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_PA200_rep1_1706.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_i20S_alone_rep4_1719.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_control_rep1_1721.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_alone_rep1_1711.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_control_rep5_1725.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD075459/Native_FT_s20S_PA200_rep1_1701.d.zip"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["Odile.Schiltz@ipbs.fr"],"submitter":["Amélie Bosc-Rosati"],"technology_type":["Mass Spectrometry","diaPASEF","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["Human","Lc-ms","Dia","Timstof"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075459"],"tissue":["Embryo","Cell Culture","Early Embryonic Cell","Kidney"],"sample_protocol":["HEK EBNA cells were lysed with 1 mL lysis buffer at pH 7.6 containing 20 mM Tris HCl, 0.02% DDM, 10 mM KCl, 10 mM EDTA, 5 mM MgCl2, and 1 tablet of protease in 50 mL (cOmplete™ ULTRA Tablets Mini EDTA-free, Roche), sonicated (Bioruptor Plus, Diagenode; 20 cycles, 30 sec on and 30 sec off) and then centrifuged at 14,000 g for 30 min at 4 °C. The supernatant was then heated in a thermomixer for 10 min at 95 °C to denature proteins. A further centrifugation at 14,000 g and 15 min at room temperature was performed to collect the heat-soluble proteins. Proteasome substrate-based activity assays with the LLVY fluorogenic peptide were used to verify that the endogenous proteasome activity was completely abolished by the heating step. The buffer was exchanged to digestion buffer (50 mM Tris, pH 7.5, 150 mM NaCl) on a 3 kDa MWCO Vivaspin 500 centrifugal concentrator. Purified s20S or i20S and PA200 were incubated  for 1 h at 4 °C at a controlled PA200:20S molar ratio of 8:1 and then 8 µg of this mixture were added to 100 ug of protein lysate and incubated 3 h at 37 °C until the reaction was stopped by adding 5 µM Bortezomib. Proteasomal peptides were subsequently separated from proteins by ultrafiltration on a 3 kDa MWCO Vivaspin.  2 µg of peptides were desalted and analyzed by nanoLC MS/MS using the TimsTOF SCP mass spectrometer as described above."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The raw data were searched and quantified with Spectronaut (Biognosis) V 20.4 using targeted peak picking strategy (DirectDIA workflow) with predicted library from UniProt human reference proteome including Frankenfield contaminants library. The following processing parameters were employed: the digest type was set as unspecific; a maximum of 3 missed cleavages was permitted; peptide length range was set at 5-52 and precursor charge states at 1-7+; N-terminal acetylation and methionine oxidation were searched as variable modifications; FDR was equal to 1% at peptide and protein level. Normalization across samples was made using the sum of the values from each sample and t-test (p-value Benjamini-Hochberg correction) was also applied."],"omics_type":["Proteomics"],"labhead":["Dr Odile Schiltz"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Toulouse, 31077, France"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["amelie.bosc-rosati@ipbs.fr"],"submitter_affiliation":["IPBS"],"submitter_country":["France"],"additional_accession":[]},"is_claimable":false,"name":"Uncovering the Role of Proteasome Activator PA200 in Regulating the Immunoproteasome","description":"The proteasome activator PA200 binds to the catalytic core of both standard proteasome (s20S) and the immunoproteasome (i20S); however, whether PA200 uses the same mechanisms to activate i20S remains unknown. Our cryo-EM structures of the singly- and doubly-capped i20S-PA200 complexes and in vitro assays here reveals that binding of the first PA200 induces an allosteric bending of the i20S and widening of the opposite unbound α-ring. This results in a higher binding occupancy of the i20S and stronger activation compared to the s20S. In addition, PA200 preferentially alters i20S proteolytic output by increasing peptide generation and shifting cleavage specificity toward caspase-like activity. We also show that in cells and tissues that express PA200, s20S and i20S, PA200 binds more efficiently to the i20S than to the s20S. Intriguingly, the expression of PA200 and the catalytic subunits of the i20S are differentially regulated, with PA200 playing a potential role in controlling the i20S subunits’ expression. This suggests that i20S function is fine-tuned by differential expression of PA200, and reveals an additional layer of i20S regulation.","dates":{"publication":"2026-05-28","submission":"2026-03-10"},"accession":"PXD075459","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:9778","NEWT:150475","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:2042546","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:185579","NEWT:43179","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:415540","NEWT:876138","NEWT:4081","NEWT:554","NEWT:98334","NEWT:426428","NEWT:237561","NEWT:6928","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:29204","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:3885","NEWT:746360","NEWT:6239","NEWT:3888","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:272559","NEWT:226186","NEWT:3641","NEWT:383379","NEWT:8782","NEWT:1263854","NEWT:1000589","NEWT:435590","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:7029","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NCBITaxon:6191","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:185431","NEWT:83332","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:44685","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:1123869","NEWT:7370","NEWT:75058","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:1094343","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:296543","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:4006","NEWT:1182590","NEWT:8726","NEWT:6669","NEWT:10090","NEWT:935293","NEWT:64152","NEWT:749200","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:645463","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:421932","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:128161","NEWT:106592","NEWT:536231","NEWT:61674","NEWT:1117957","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:1424507","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:180066","NEWT:67767","NEWT:46835","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:1416333","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NCBITaxon:2759","NEWT:1911079","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:27606","NEWT:59202","NEWT:9975","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:411483","NEWT:884019","NEWT:411490","NEWT:169963","NEWT:36329","NEWT:1147787","NCBITaxon:3044782","NEWT:72407","NEWT:476272","NEWT:349741","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:641501","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:9721","NEWT:1450511","NEWT:360094","NEWT:470","NEWT:411901","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:9838","NCBITaxon:9615","NCBITaxon:5811","NEWT:58334","NEWT:411464","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:411460","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:178876","NEWT:9940","NEWT:327160","NEWT:573","NEWT:521001","NEWT:9031","NEWT:1274420","NEWT:7091","NEWT:578458"]}}