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Bourguet"],"technology_type":["Mass Spectrometry","Chemical cross-linking coupled with mass spectrometry proteomics"],"software":["Not available"],"submitter_keywords":["Hdx-ms","Pi3k","Structural characterization","Xl-ms","Cryo-em","Autophagy"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD079187"],"sample_protocol":["For the sample with soluble GABARAP, 4 µM of PtdIns3K-C1 were incubated with 50 µM of GABARAP (1−116) for 30 min on ice in a buffer containing 20 mM HEPES pH8, 150 mM NaCl and 0.5 mM TCEP. For the sample containing LUVs, the vesicles were coated with GABARAP (L117C) by a maleimide reaction as detailed above. PtdIns3K-C1 was then added to the concentrated LUVs at a concentration of 3.6 µM, for 50 µL final volume, and incubated on ice for 30 min. Protein crosslinking reactions were carried out by adding 2 mM of sulfo-SDA to the protein mixture, with 5 min incubation on ice, followed by 10 s 365 nm UV radiation from a home build UV LED setup. Crosslinking reactions were quenched with the addition of ammonium bicarbonate to a final concentration of 50 mM. The quenched solution was reduced with 5 mM DTT and alkylated with 20 mM idoacetamide. SP3 protocol (Batth T.S. et al., MCP, 2019 ; Hughes C.S. et al., Nature protocols, 2019) was used to clean-up and buffer exchange the reduced and alkylated protein, shortly, proteins were washed with ethanol using magnetic beads for protein capture and binding. The proteins were resuspended in 100 mM NH4HCO3 and were digested with trypsin (Promega) at an enzyme-to-substrate ratio of 1:20, and protease max 0.1% (Promega). Digestion was carried out overnight at 37 °C. Clean-up of peptide digests was carried out with HyperSep SpinTip P-20 (ThermoScientific) C18 columns, using 60 % Acetonitrile as the elution solvent. Peptides were then evaporated to dryness via Speed Vac Plus (Savant). Dried peptides were resupended in 30 % acetonitrile and were fractionated via size exclusion chromatography using a Superdex 30 Increase 3.2/300 column (GE heathcare) at a flow rate of 20 µL/min using 30% (v/v) ACN and 0.1 % (v/v) TFA as a mobile phase. Fractions were taken every 5 min, and the 2nd to 7th fractions containing crosslinked peptides were collected. Dried peptides were suspended in 3% (v/v) Acetonitrile and 0.1 % (v/v) formic acid and analysed by nano-scale capillary LC-MS/MS using an Ultimate U3000 HPLC (ThermoScientific) to deliver a flow of 300 nL/min. Peptides were trapped on a C18 Acclaim PepMap100 5 μm, 0.3 μm x 5 mm cartridge (ThermoScientific) before separation on Aurora Ultimate C18, 1.7 μm, 75 μm x 25 cm (Ionopticks). Peptides were eluted on optimized gradients of 90 min and interfaced via an EasySpray ionization source to a tribrid quadrupole Orbitrap mass spectrometer (Orbitrap Eclipse, ThermoScientific) equipped with FAIMS. MS data were acquired in data dependent mode with a Top-25 method, high resolution scans full mass scans were carried out (R=120,000, m/z 400–1550) followed by higher energy collision dissociation with stepped collision energy range 21, 30, 34 % normalized collision energy. The tandem mass spectra were recorded (R=60,000, isolation window m/z 1, dynamic exclusion 50 s). Mass spectrometry measurements were cycled for 3 s durations between FAIMS CV –45, and –60 V."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Cross linking data analysis was done by converting Xcalibur raw files to MGF files using ProteoWizard (Chambers M.C. et al., Nature Biotechnology, 2012) and crosslinks were analysed by XiSearch {Mendes, 2019 #386}. Search conditions used 3 maximum missed cleavages with a minimum peptide length of 5. Variable modifications used were carbmidomethylation of cysteine (57.02146 Da) and Methionine oxidation (15.99491 Da). False discovery rate was set to 5%. Data was imported in XiView (Combe C.W. et al., Journal of Molecular Biology, 2024) for manual filtering, and exported to the PDB 9TW2 in PyMOL 2.5.4 (Schrödinger)."],"omics_type":["Proteomics"],"labhead":["Roger Lee Williams"],"instrument_platform":[""],"labhead_affiliation":["MRC - Laboratory of Molecular Biology"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["mbourguet@mrc-lmb.cam.ac.uk"],"submitter_affiliation":["MRC Laboratory of Molecular Biology"],"submitter_country":["United Kingdom"],"additional_accession":[]},"is_claimable":false,"name":"A GABARAP−PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation","description":"Macroautophagy/autophagy is a cellular process enabling degradation of intracellular components during starvation. In mammalian cells, autophagosomes can reach diameters of over 1000 nm within 30 min after triggering starvation, but how such substantial amounts of membranes can be synthesized within a brief time remains elusive. A protein complex central to the phagophore initiation is the lipid kinase PIK3C3-Complex 1 (PtdIns3K-C1), which produces phosphatidylinositol-3-phosphate (PtdIns3P). PtdIns3P recruits a variety of downstream proteins, among which is PtdIns3P-binding WIPI2 that facilitates lipidation of mammalian ATG8 (mATG8) family proteins on phagophores. Here we show that upon acute inhibition of mATG8 lipidation in cells, there is no further accumulation of WIPI2, suggesting a feedback loop between mATG8s and PtdIns3P production. The role of PtdIns3K-C1 in this feedback was demonstrated by in vitro experiments where recombinant membrane-coupled mATG8s bind to and potently activate PtdIns3K-C1, with GABARAP being the most potent activator among all mATG8s. By a combination of cryo-electron microscopy, structural mass spectrometry, activity assays and mutagenesis, we show that GABARAP binds two sites in PtdIns3K-C1, with one site showing an atypical bipartite interaction with the mATG8. We also confirm both sites are essential for GABARAP to activate PtdIns3K-C1. We propose that once GABARAP is indirectly recruited by PtdIns3P generated by basal activity of PtdIns3K-C1, a positive feedback loop is formed where PtdIns3K-C1 interacts with GABARAP and becomes activated to produce more PtdIns3P, thereby further stimulating GABARAP lipidation. This mechanism would be central for autophagosome biogenesis, where enlarged membranes need to be synthesized within a brief period.","dates":{"publication":"2026-07-02","submission":"2026-06-02"},"accession":"PXD079187","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:8655","NEWT:5147","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:7742","NEWT:196627","NEWT:200308","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810","NCBITaxon:5693","NEWT:28995","NEWT:1392998","NEWT:380394","NEWT:226900","NEWT:1266738","NEWT:231490","NEWT:244704","NEWT:7725","NEWT:9909","NEWT:9902","NEWT:430615","NEWT:563041","NEWT:72664","NEWT:36599","NEWT:41949","NEWT:326423","NEWT:452467","NEWT:198822","NEWT:36111","NEWT:326424","NEWT:1678078","NEWT:7499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