{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075969/SuppTable5_CagM_DEK.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075969/SuppTable4_CagM_NTD-EK.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075969/checksum.txt"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075969/CagM_NTD-EK_DEK_raw.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["shannon-au@cuhk.edu.hk"],"submitter":["Chin Yu Mok"],"technology_type":["Mass Spectrometry","MSE"],"software":["Not available"],"submitter_keywords":["Type iv secretion system","H. pylori","Cagm"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075969"],"sample_protocol":["HDX-MS experiments were performed on a nanoACQUITY UPLC system coupled with Synapt G2-Si Mass Spectrometer (Waters Corporation). To prepare reactions comparing wild-type and mutated CagM (NTD-EK and DEK), 2 μl of protein was mixed with 48 μl of deuterated buffer containing 20 mM HEPES, 300 mM NaCl, pD 7.5 and 96% D2O, yielding a protein concentration of 2 μM. The mixtures were incubated for various time periods (0.5, 1, 10, 60 and 120 min) at room temperature and quenched by adding equal volume of ice-cold quenching buffer, resulting in a final pH of 2.5. For non-deuterated samples, same procedures were performed by replacing deuterated buffer with buffer containing 20 mM HEPES, 300 mM NaCl, pH 7.5. Quenched protein mixtures were immediately digested online by Waters Enzymate Protein Pepsin column (300 Å, 5 µm, 2.1 mm X 30 mm) at a flow rate of 100 μl/min. The peptides were trapped on a Waters ACQUITY UPLC BEH C18 VanGuard Pre-column (130 Å, 1.7 µm, 2.1 mm X 5 mm) for 3 min before being applied to a Waters ACQUITY Premier BEH C18 column (1.7 µm, 2.1 x 100 mm). Peptides were eluted in an acetonitrile gradient, in which solvent A was 0.1% formic acid and solvent B was 0.1% formic acid in acetonitrile. The whole trapping and chromatographic process was kept at 0 °C to minimize back exchange. Purified peptides were electrosprayed onto the mass spectrometer in MSE mode and the mass spectra were acquired in the range of 100-3000 m/z. The instrument was calibrated using sodium iodide and lock mass accuracy correction was made by intermittent infusion of leucine enkephalin. Each sample was performed in triplicate across all time points."],"repository":["Pride"],"modification":[""],"quantification_method":["Not available"],"data_protocol":["Peptides in non-deuterated samples were identified using ProteinLynx Global Server (Waters). They were searched against the database containing their primary sequences and filtered by the following parameters: intensity > 1000, number of product ions per amino acids > 0.25, PLGS score > 6 and precursor ion (MH+) mass error < 10 ppm. Data was manually inspected via DynamX (Waters). Relative deuterium uptake between two states were determined by calculating the deuterium uptake differences of the identical peptides. Statistical significance was determined by 95% confidence interval."],"omics_type":["Proteomics"],"labhead":["Shannon Wing Ngor Au"],"instrument_platform":[""],"labhead_affiliation":["School of Life Sciences, The Chinese University of Hong Kong"],"submission_type":["PARTIAL"],"species":["Helicobacter Pylori G27"],"publication":["Not available"],"submitter_mail":["yukomokk14@gmail.com"],"submitter_affiliation":["The Chinese University of Hong Kong"],"submitter_country":["Hong Kong"],"additional_accession":[]},"is_claimable":false,"name":"Conformational dynamics of CagM homo-oligomerization by HDX-MS","description":"Cag type IV secretion system (CagT4SS) mediates the translocation of a wide spectrum of substrates including oncoprotein CagA to host cells and plays an indispensable role in the pathogenesis of Helicobacter pylori. CagM, one of the central cylinder components responsible for initiating the assembly of CagT4SS, is able to undergo high-order homo-oligomerization. Two CagM mutants, NTD-EK (E29K/K31E/K32E/E33K/E35K/E36K) and DEK (D183E/E184K/E185K), deficient in high-order oligomerization were generated. Here, we performed differential HDX-MS analysis on wild-type, to characterize the interface involved in homo-oligomerization. Our findings reveal the significance of CagM homo-oligomerization on facilitating CagT4SS assembly.","dates":{"publication":"2026-06-14","submission":"2026-03-21"},"accession":"PXD075969","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:515849","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:143361","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:294381","NEWT:197","NEWT:1390363","NEWT:77133","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:556182","NEWT:1270","NEWT:374990","NEWT:498217","NEWT:156471","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:156476","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:1143","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:296543","NEWT:316435","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:105023","NEWT:866628","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NEWT:8175","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:2850","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:46704","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:269796","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:9483","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:759272","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:180923","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:527796","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:43665","NEWT:1266464","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:375451","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:1328426","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:327159","NEWT:178876","NEWT:1660","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1821314","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:5286","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:9644","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:27592","NEWT:98334","NEWT:426428","NEWT:63459","NEWT:1276815","NEWT:36185","NEWT:588858","NEWT:9639","NCBITaxon:11071","NEWT:242231","NEWT:7574","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