DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ sawa_makarska-2014-1 in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260961X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-2 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by comassie molecular weight estimation by coomasie staining weight by comassie Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260959X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-3 in vitro In vitro pull down pull down predetermined predetermined participant predetermined Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260964X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-4 in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260969X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-5 in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260967X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-6 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260962X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-7 in vitro In vitro pull down pull down predetermined predetermined participant predetermined Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260965X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-8 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by comassie molecular weight estimation by coomasie staining weight by comassie Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260960X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-9 in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260966X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-10 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260963X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation sawa_makarska-2014-11 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. DIP original experiment: DIP-260968X Nature cell biology 2014 IMEx Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Sawa-Makarska J., Abert C., Romanov J., Zens B., Ibiricu I., Martens S. Only protein-protein interactions imex curation atg19_yeast Autophagy-related protein 19 Cytoplasm-to-vacuole targeting protein 19 ATG19 CVT19 YOL082W O0980 YOL01 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNNSKTNQQMNTSMGYPLTVYDECNKFQLIVPTLDANIMLWCIGQLSLLNDSNGCKHLFWQPNDKSNVRILLNNYDYGHLFKYLQCQRKCSVYIGEGTLKKYNLTISTSFDNFLDLTPSEEKESLCREDAHEDPVSPKAGSEEEISPNSTSNVVVSRECLDNFMKQLLKLEESLNKLELEQKVTNKEPNHRISGTIDIPEDRSELVNFFTELKTVKQLEDVFQRYHDYERLSQECDSKTEIASDHSKKETKIEVEPPNERSLQITMNQRDNSLYFQLFNNTNSVLAGNCKLKFTDAGDKPTTQIIDMGPHEIGIKEYKEYRYFPYALDLEAGSTIEIENQYGEVIFLGKYGSSPMINLRPPSRLSAESLQASQEPFYSFQIDTLPELDDSSIISTSISLSYDGDDNEKALTWEEL B49DA1DF83A04070 atg8_yeast Autophagy-related protein 8 ATG8 APG8 AUT7 YBL078C YBL0732 CVT5 Autophagy-related ubiquitin-like modifier ATG8 Cytoplasm to vacuole targeting protein 5 protein protein yeast Saccharomyces cerevisiae Baker's yeast MKSTFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGENTFGR 1246CEFF5A038819 atg34_yeast Autophagy-related protein 34 ATG34 O0957 YOL083W ATG19-B protein protein yeast Saccharomyces cerevisiae Baker's yeast MKIAVETTLFDFFVIDQFKKSTFSAPNTKVDTIKGCINKFIEQFNVYDEQHIFWQPPGKSNVRLLSNANDFGQLGNFLHKKIKCNIFIGEEALRKYDLNICGPYDKFVENSDPSVKKVVNRDDVMLSRKCLNIISEQLSILEKSISKAQNQVLQSSEVEGKKCIILPEDKPELIKFFSKFETSVQLQEVYEGYKVYEKLLQKFGGQKKRMESFLNENTPMSGAEAIKQINISEELKEKGERLTTPNDPLLHVEVSNEDNSLHFILYNKTNIIIPGNCTFEFSSQISEVFSIKMGPHEIGIKGQKELWFFPSLPTPLSNYTMKVVNQDGETILVGKCADSNEITLKSPLASFSTGSFQTGSFHTLQDPTNVFRADALSSPDESSIMSTPFLGETDEVYNSGSTLSRPFTWEEI 5F339CC6AC2824D5 ampl_yeast Vacuolar aminopeptidase 1 APE1 API Aminopeptidase yscI LAP4 Leucine aminopeptidase IV Lysosomal aminopeptidase III Polypeptidase Vacuolar aminopeptidase I YSC1 YKL455 YKL103C protein protein yeast Saccharomyces cerevisiae Baker's yeast MEEQREILEQLKKTLQMLTVEPSKNNQIANEEKEKKENENSWCILEHNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPDEEGNEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL 702A8C88A2124C24 atg11_yeast Autophagy-related protein 11 Cytoplasm to vacuole targeting protein 9 ATG11 CVT9 YPR049C YP9499.07c protein protein yeast Saccharomyces cerevisiae Baker's yeast MADADEYSTAPTQQEITPLQTTATIINAISGECITTNVDFFVSLDKFKQFIARKWKIPPDQLLILLPYGNKLKPSMFKELLINRSFTLNDFYVYDRRLFSLVSKPTPTNLLTSKDSNPMNSPNSNDLTETLEYLIKNSHISQYQGSDTIMIKPMPSPLEDADVDLSRLNYHSVTSLLTTNLGWLSALEIDVHYFKSLIPDIIAHIKRIFDGLTVCSQYLKLYCFDVESLYNSNVQFLNQLVDNGMTSKWEKCFNDTLSKLTALEGDSLQKFINIESLLENEKSVKILNHSINGKLNKIKREIDENASFRDIITVNIDRLRQMFTPNESKFELEDQMAESFEVLVSEMRTRSRNVLDKEEEEFNSQEFLKSMNVMLEKDKKESVKTLFTISQALYSQIGELIDLKKSLQKHAVAILGNIAFTQMEILGIKRLLLNECNKDLELYKKYEVEFAQVEDLPLIYGLYLIEKYRRLSWFQQILSFISNFNQDLELFKQNELRTRNKWVKNFGSIATVFCEDLLSSSDFKRLNEYHSHTSPPNEDEEDENENSIANYRQDLVKVSQAIDNYMTQIKETDVSEPIIDLLSKTLFETKRFHIIYSNFKNNNNNSSNGNSISPEGSIALKSDDVVKGYKTRIKKLESLLHEFQYSDIGHWPQGVLNTHLKPFRGSATSINKKKFLGASVLLEPANISEVNIDSVSQANNHQIQELESNVDDLLHQLQLLKEENNRKSMQISEMGKKISDLEVEKTAYRETLTNLNQELARLTNEEQSHRTEIFTLNASFKKQLNDIISQDNEKIEKLTGDYDDVSKSRERLQMDLDESNKKHEQEVNLLKADIERLGKQIVTSEKSYAETNSSSMEKGEKFETIPLAEDPGRENQISAYTQTLQDRIFDIISTNIFILENIGLLLTFDNNNNIQIRRVKGLKKGTAQSNILDESTQMLDAHDNSLIKSPVFQKLKDEYELIKSVANGSEKDTQQSIFLGNITQLYDNKLYEVAVIRRFKDIETLAKKLTKENKIKRTLLERFQREKVTLRNFQIGDLALFLPTRENVNSVGSMSSSTSSLSSSFSSVDLSTPPPLDAMSIQSSPSVIHSNVINQASISGRDKNKLMRPWAAFTAFEESTRYFLKDEKGLTKGKEWFVGRIVTLEHFVADSPSNNPFRLPKGSVWFQVTAVVVSYQGV A904B92E9AE79449 atg19-atg8-1 3264556 N/A 3264567 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3264568 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false atg19-atg8-2 3264557 N/A 3264567 unspecified role unspecified role unspecified role unspecified role Region 365-415 Region 365-415 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false P35193:p.Trp412Ala W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3264568 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false Deletion of region 408-415 decreased the interaction rate/strength. atg34-atg8-1 3264558 N/A 3264569 unspecified role unspecified role bait bait GST-tag GST-tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli N/A 3264568 unspecified role unspecified role prey prey ecolx Escherichia coli direct interaction direct interaction false false false atg8-atg19-1 3264559 N/A 3264567 unspecified role unspecified role prey prey P35193:p.[Phe376Ala;Phe379Ala;Pro385Ala;Glu386Ala;Trp412Ala] F376A/F379A/P385A/E386A/W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe376Ala;Phe379Ala;Trp412Ala] F376A/F379A/W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe376Ala;Phe379Ala] F376A/F379A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Region 1-384 Region 1-384 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3264568 unspecified role unspecified role bait bait GST-tag GST-tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli direct interaction direct interaction false false false ape1-atg8-1 3264560 N/A 3264568 unspecified role unspecified role prey prey ecolx Escherichia coli N/A 3264570 unspecified role unspecified role bait bait Region 1-45 Region 1-45 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false GST-tag GST-tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli physical association physical association false false false atg11-atg34-1 3264561 N/A 3264569 unspecified role unspecified role prey prey yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3264571 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false atg19-atg8-3 3264562 N/A 3264567 unspecified role unspecified role bait bait GST-tag GST-tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Region 376-415 Region 376-415 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false P35193:p.Trp412Ala W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false Region 1-384 Region 1-384 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe376Ala;Phe379Ala;Pro385Ala;Glu386Ala;Trp412Ala] F376A/F379A/P385A/E386A/W412A mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P35193:p.[Pro385Ala;Glu386Ala;Trp412Ala] P385A/E386A/W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe376Ala;Phe379Ala;Trp412Ala] F376A/F379A/W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe376Ala;Phe379Ala] F376A/F379A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe379Ala;Trp412Ala] F379A/W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3264568 unspecified role unspecified role prey prey ecolx Escherichia coli direct interaction direct interaction false false false atg34-atg8-2 3264563 N/A 3264569 unspecified role unspecified role unspecified role unspecified role Q12292:p.Trp409Ala W409A mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3264568 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false ape1-atg19-1 3264564 N/A 3264570 unspecified role unspecified role bait bait Region 1-45 Region 1-45 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false GST-tag GST-tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli N/A 3264567 unspecified role unspecified role prey prey ecolx Escherichia coli direct interaction direct interaction false false false atg11-atg19-2 3264565 N/A 3264567 unspecified role unspecified role prey prey yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3264571 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false atg8-atg19-2 3264566 N/A 3264567 unspecified role unspecified role prey prey P35193:p.Trp412Ala W412A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe376Ala;Phe379Ala;Trp412Ala] F376A/F379A/W412A mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P35193:p.[Phe376Ala;Phe379Ala;Pro385Ala;Glu386Ala;Trp412Ala] F376A/F379A/P385A/E386A/W412A mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Myc-tag Myc-tag myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3264568 unspecified role unspecified role bait bait GFP-tag GFP-tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false