{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample07_Crosslinks.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample04_Crosslinks.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample06_Crosslinks.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample02_Crosslinks.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample01_Crosslinks.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample05_Crosslinks.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample03_Crosslinks.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample08_Crosslinks.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample06.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample08.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample04.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063587/202401217_EXPL6_Neo_BaSt_SA_Orbi5445_sample02.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["Jae@genzentrum.lmu.de"],"submitter":["Barbara Steigenberger"],"technology_type":["Mass Spectrometry","Chemical cross-linking coupled with mass spectrometry proteomics"],"software":[""],"submitter_keywords":["Xl-ms","Heme","Dele1","Hri"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063587"],"sample_protocol":["In vitro crosslinking and XL-MS To assess confirmational changes occurring in HRI upon heme displacement and kinase activation by S-DELE1, Strep-tagged HRI purified from human cells in presence or absence of S-DELE1 was crosslinked for 30 minutes at room temperature with 125uM DSS. The crosslinking reaction was terminated by addition of 25mM TRIS/HCl pH7.5 for ten minutes on ice. Samples were snap frozen in liquid nitrogen and subjected to XL-MS analysis. Sample preparation  Crosslinked proteins were denatured by the addition of 4 M urea in 50 mM Tris buffer. To reduce and alkylate disulfides, 10 mM tris(2-carboxyethyl)phosphine (TCEP, Thermo Fisher Scientific) and 40 mM 2-chloroacetamide (CAA, Sigma-Aldrich) were added. The samples were incubated at 37°C for 20 minutes. Following incubation, they were diluted 1:3 with MS-grade water (VWR). Proteins were enzymatically digested overnight at 37°C using 1 µg of LysC and 2 µg of trypsin (Promega). After digestion, the reaction was acidified to a final concentration of 1% trifluoroacetic acid (TFA, Merck), and peptides were desalted using Sep-Pak C18 1cc vacuum cartridges (Waters). A total of 200 ng of peptides was loaded onto Evotips Pure (Evosep). LC-MS/MS data acquisition Peptides were then eluted from the Evotips onto a 15-cm PepSep C18 column (15 cm × 150 µm, 1.5 µm particle size, Bruker Daltonics) using the Evosep One HPLC system, employing the 30 samples per day (SPD) method. Mass spectrometry analysis was carried out on an Orbitrap Exploris 480 (Thermo Fisher), operated in data-dependent acquisition mode. Full MS scans were collected from m/z 300 to 1650 Th at a resolution of 60,000 (at m/z 200 Th). The top 15 most intense precursor ions were selected for fragmentation using stepped higher-energy C-trap dissociation (HCD) at normalized collision energies of 19, 27, and 35. MS2 spectra were acquired with a resolution of 30,000 (at m/z 200 Th) across a dynamic m/z range. Normalized automatic gain control (AGC) targets were set to 300% for MS1 and 100% for MS2, with a maximum injection time of 25 ms for MS1 and \"auto\" for MS2. Ions with a charge state of +2 were excluded to prioritize crosslinked precursors."],"repository":["pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Data analysis Raw data were analyzed using Proteome Discoverer (version 2.5.0.400), incorporating XlinkX/PD nodes (Klykov et al., 2018). Crosslinked peptides were identified via database search against a FASTA file containing the relevant protein sequences. DSS/BS3 was selected as the crosslinking reagent. Carbamidomethylation of cysteines was set as a static modification, while oxidation of methionines and N-terminal acetylation were defined as variable modifications. Trypsin/P was used as the specified protease, allowing for up to two missed cleavages. Peptide identifications were accepted with a minimum score of 40 and a delta score of at least 4. A 1% false discovery rate (FDR) at the peptide level was applied for filtering."],"omics_type":["Proteomics"],"labhead":["Lucas Jae"],"instrument_platform":[""],"labhead_affiliation":["Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["steigenberger@biochem.mpg.de"],"publication":["Not available"],"submitter_affiliation":["MPI of Biochemistry"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Association of heme bound HRI with S-DELE1 promotes structural re-arrangements within the HRI kinase domain","description":"This dataset assesses structural changes occurring in human, heme-bound HRI upon association with S-DELE1. To this end, human HRI and S-DELE1 were expressed EIF2alpha phosphorylation-resistent cells supplemented with hemin. HRI was affinity purified, crosslinked with DSS, and structural changes in HRI were assessed by MS. The data set identifies S-DELE1 induced structural changes in the C-terminal region and the kinase insert of HRI, as well as domains of HRI that are in structural proximity to S-DELE1.","dates":{"publication":"2026-05-07","submission":"2025-05-04"},"accession":"PXD063587","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:150475","NEWT:9417","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:4081","NEWT:876138","NEWT:554","NEWT:98334","NEWT:237561","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:8782","NEWT:1000589","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: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:931281","NEWT:7029","NEWT:1283300","NEWT:334747","NEWT:61235","NCBITaxon:79824","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: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:83906","NEWT:6282","NEWT:1134506","NEWT:575584","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:1182590","NEWT:8726","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:4120","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:106592","NEWT:1117957","NEWT:9913","NEWT:1432138","NEWT:10312","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:5664","NEWT:2157","NEWT:146479","NEWT:10306","NEWT:1911079","NEWT:8022","NEWT:145943","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:59202","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:1147787","NEWT:72407","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:1450511","NEWT:470","NEWT:84023","NEWT:9838","NCBITaxon:9615","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:33952","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:9940","NEWT:573","NEWT:9031","NEWT:1274420","NEWT:7091"]}}