IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ ashkenazi-2017-4 human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western Ashkenazi A., Bento CF., Ricketts T., Vicinanza M., Siddiqi F., Pavel M., Squitieri F., Hardenberg MC., Imarisio S., Menzies FM., Rubinsztein DC. The authors have stated that HA-AR and eGFP-ATN1 (as used in Extended Data figure 10) are of Human origin. dcr1000@cam.ac.uk Nature 2017 imex curation Only protein-protein interactions ashkenazi-2017-3 human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Ashkenazi A., Bento CF., Ricketts T., Vicinanza M., Siddiqi F., Pavel M., Squitieri F., Hardenberg MC., Imarisio S., Menzies FM., Rubinsztein DC. The authors have stated that HA-AR and eGFP-ATN1 (as used in Extended Data figure 10) are of Human origin. dcr1000@cam.ac.uk Nature 2017 imex curation Only protein-protein interactions ashkenazi-2017-1 human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Ashkenazi A., Bento CF., Ricketts T., Vicinanza M., Siddiqi F., Pavel M., Squitieri F., Hardenberg MC., Imarisio S., Menzies FM., Rubinsztein DC. The authors have stated that HA-AR and eGFP-ATN1 (as used in Extended Data figure 10) are of Human origin. dcr1000@cam.ac.uk Nature 2017 imex curation Only protein-protein interactions ashkenazi-2017-2 in vitro In vitro deubiquitinase assay deubiquitinase assay deubiquitinase assay anti tag western anti tag western blot anti tag western Ashkenazi A., Bento CF., Ricketts T., Vicinanza M., Siddiqi F., Pavel M., Squitieri F., Hardenberg MC., Imarisio S., Menzies FM., Rubinsztein DC. The authors have stated that HA-AR and eGFP-ATN1 (as used in Extended Data figure 10) are of Human origin. dcr1000@cam.ac.uk Nature 2017 imex curation Only protein-protein interactions becn1_human Beclin-1 Coiled-coil myosin-like BCL2-interacting protein Protein GT197 BECN1 GT197 protein protein human Homo sapiens Human MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQLQMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK isolated polyq stretch_q35 peptide peptide polypeptide oligopeptide oligopeptide polypeptide human Homo sapiens Human QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ p54252-1 Ataxin-3 ATXN3 ATX3 MJD MJD1 SCA3 Machado-Joseph disease protein 1 Spinocerebellar ataxia type 3 protein MJD1a protein protein human Homo sapiens Human MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVHKTDLERVLEANDGSGMLDEDEEDLQRALALSRQEIDMEDEEADLRRAIQLSMQGSSRNISQDMTQTSGTNLTSEELRKRREAYFEKQQQKQQQQQQQQQQGDLSGQSSHPCERPATSSGALGSDLGKACSPFIMFATFTLYLTYELHVIFALHYSSFPL Variant in position: 349:YELHVIFALHYSSFPL->Missing (in short isoform 1, due to a stop-gain single nucleotide polymorphism, has reduced half-life due to increased proteasomal degradation, has reduced solubility and increased tendency to form aggregates, increased localization to the nucleus). isolated polyq stretch_q81 protein protein human Homo sapiens Human QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ hd_human Huntingtin HTT IT15 HD Huntington disease protein protein protein human Homo sapiens Human MATLEKLMKAFESLKSFQQQQQQQQQQQQQQQQQQQQQPPPPPPPPPPPQLPQPPPQAQPLLPQPQPPPPPPPPPPGPAVAEEPLHRPKKELSATKKDRVNHCLTICENIVAQSVRNSPEFQKLLGIAMELFLLCSDDAESDVRMVADECLNKVIKALMDSNLPRLQLELYKEIKKNGAPRSLRAALWRFAELAHLVRPQKCRPYLVNLLPCLTRTSKRPEESVQETLAAAVPKIMASFGNFANDNEIKVLLKAFIANLKSSSPTIRRTAAGSAVSICQHSRRTQYFYSWLLNVLLGLLVPVEDEHSTLLILGVLLTLRYLVPLLQQQVKDTSLKGSFGVTRKEMEVSPSAEQLVQVYELTLHHTQHQDHNVVTGALELLQQLFRTPPPELLQTLTAVGGIGQLTAAKEESGGRSRSGSIVELIAGGGSSCSPVLSRKQKGKVLLGEEEALEDDSESRSDVSSSALTASVKDEISGELAASSGVSTPGSAGHDIITEQPRSQHTLQADSVDLASCDLTSSATDGDEEDILSHSSSQVSAVPSDPAMDLNDGTQASSPISDSSQTTTEGPDSAVTPSDSSEIVLDGTDNQYLGLQIGQPQDEDEEATGILPDEASEAFRNSSMALQQAHLLKNMSHCRQPSDSSVDKFVLRDEATEPGDQENKPCRIKGDIGQSTDDDSAPLVHCVRLLSASFLLTGGKNVLVPDRDVRVSVKALALSCVGAAVALHPESFFSKLYKVPLDTTEYPEEQYVSDILNYIDHGDPQVRGATAILCGTLICSILSRSRFHVGDWMGTIRTLTGNTFSLADCIPLLRKTLKDESSVTCKLACTAVRNCVMSLCSSSYSELGLQLIIDVLTLRNSSYWLVRTELLETLAEIDFRLVSFLEAKAENLHRGAHHYTGLLKLQERVLNNVVIHLLGDEDPRVRHVAAASLIRLVPKLFYKCDQGQADPVVAVARDQSSVYLKLLMHETQPPSHFSVSTITRIYRGYNLLPSITDVTMENNLSRVIAAVSHELITSTTRALTFGCCEALCLLSTAFPVCIWSLGWHCGVPPLSASDESRKSCTVGMATMILTLLSSAWFPLDLSAHQDALILAGNLLAASAPKSLRSSWASEEEANPAATKQEEVWPALGDRALVPMVEQLFSHLLKVINICAHVLDDVAPGPAIKAALPSLTNPPSLSPIRRKGKEKEPGEQASVPLSPKKGSEASAASRQSDTSGPVTTSKSSSLGSFYHLPSYLKLHDVLKATHANYKVTLDLQNSTEKFGGFLRSALDVLSQILELATLQDIGKCVEEILGYLKSCFSREPMMATVCVQQLLKTLFGTNLASQFDGLSSNPSKSQGRAQRLGSSSVRPGLYHYCFMAPYTHFTQALADASLRNMVQAEQENDTSGWFDVLQKVSTQLKTNLTSVTKNRADKNAIHNHIRLFEPLVIKALKQYTTTTCVQLQKQVLDLLAQLVQLRVNYCLLDSDQVFIGFVLKQFEYIEVGQFRESEAIIPNIFFFLVLLSYERYHSKQIIGIPKIIQLCDGIMASGRKAVTHAIPALQPIVHDLFVLRGTNKADAGKELETQKEVVVSMLLRLIQYHQVLEMFILVLQQCHKENEDKWKRLSRQIADIILPMLAKQQMHIDSHEALGVLNTLFEILAPSSLRPVDMLLRSMFVTPNTMASVSTVQLWISGILAILRVLISQSTEDIVLSRIQELSFSPYLISCTVINRLRDGDSTSTLEEHSEGKQIKNLPEETFSRFLLQLVGILLEDIVTKQLKVEMSEQQHTFYCQELGTLLMCLIHIFKSGMFRRITAAATRLFRSDGCGGSFYTLDSLNLRARSMITTHPALVLLWCQILLLVNHTDYRWWAEVQQTPKRHSLSSTKLLSPQMSGEEEDSDLAAKLGMCNREIVRRGALILFCDYVCQNLHDSEHLTWLIVNHIQDLISLSHEPPVQDFISAVHRNSAASGLFIQAIQSRCENLSTPTMLKKTLQCLEGIHLSQSGAVLTLYVDRLLCTPFRVLARMVDILACRRVEMLLAANLQSSMAQLPMEELNRIQEYLQSSGLAQRHQRLYSLLDRFRLSTMQDSLSPSPPVSSHPLDGDGHVSLETVSPDKDWYVHLVKSQCWTRSDSALLEGAELVNRIPAEDMNAFMMNSEFNLSLLAPCLSLGMSEISGGQKSALFEAAREVTLARVSGTVQQLPAVHHVFQPELPAEPAAYWSKLNDLFGDAALYQSLPTLARALAQYLVVVSKLPSHLHLPPEKEKDIVKFVVATLEALSWHLIHEQIPLSLDLQAGLDCCCLALQLPGLWSVVSSTEFVTHACSLIYCVHFILEAVAVQPGEQLLSPERRTNTPKAISEEEEEVDPNTQNPKYITAACEMVAEMVESLQSVLALGHKRNSGVPAFLTPLLRNIIISLARLPLVNSYTRVPPLVWKLGWSPKPGGDFGTAFPEIPVEFLQEKEVFKEFIYRINTLGWTSRTQFEETWATLLGVLVTQPLVMEQEESPPEEDTERTQINVLAVQAITSLVLSAMTVPVAGNPAVSCLEQQPRNKPLKALDTRFGRKLSIIRGIVEQEIQAMVSKRENIATHHLYQAWDPVPSLSPATTGALISHEKLLLQINPERELGSMSYKLGQVSIHSVWLGNSITPLREEEWDEEEEEEADAPAPSSPPTSPVNSRKHRAGVDIHSCSQFLLELYSRWILPSSSARRTPAILISEVVRSLLVVSDLFTERNQFELMYVTLTELRRVHPSEDEILAQYLVPATCKAAAVLGMDKAVAEPVSRLLESTLRSSHLPSRVGALHGVLYVLECDLLDDTAKQLIPVISDYLLSNLKGIAHCVNIHSQQHVLVMCATAFYLIENYPLDVGPEFSASIIQMCGVMLSGSEESTPSIIYHCALRGLERLLLSEQLSRLDAESLVKLSVDRVNVHSPHRAMAALGLMLTCMYTGKEKVSPGRTSDPNPAAPDSESVIVAMERVSVLFDRIRKGFPCEARVVARILPQFLDDFFPPQDIMNKVIGEFLSNQQPYPQFMATVVYKVFQTLHSTGQSSMVRDWVMLSLSNFTQRAPVAMATWSLSCFFVSASTSPWVAAILPHVISRMGKLEQVDVNLFCLVATDFYRHQIEEELDRRAFQSVLEVVAAPGSPYHRLLTCLRNVHKVTTC atn1_human Atrophin-1 ATN1 DRPLA Dentatorubral-pallidoluysian atrophy protein D12S755E protein protein human Homo sapiens Human MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVEEASTPKVNKQGRSEEISESESEETNAPKKTKTEQELPRPQSPSDLDSLDGRSLNDDGSSDPRDIDQDNRSTSPSIYSPGSVENDSDSSSGLSQGPARPYHPPPLFPPSPQPPDSTPRQPEASFEPHPSVTPTGYHAPMEPPTSRMFQAPPGAPPPHPQLYPGGTGGVLSGPPMGPKGGGAASSVGGPNGGKQHPPPTTPISVSSSGASGAPPTKPPTTPVGGGNLPSAPPPANFPHVTPNLPPPPALRPLNNASASPPGLGAQPLPGHLPSPHAMGQGMGGLPPGPEKGPTLAPSPHSLPPASSSAPAPPMRFPYSSSSSSSAAASSSSSSSSSSASPFPASQALPSYPHSFPPPTSLSVSNQPPKYTQPSLPSQAVWSQGPPPPPPYGRLLANSNAHPGPFPPSTGAQSTAHPPVSTHHHHHQQQQQQQQQQQQQQQQQQQHHGNSGPPPPGAFPHPLEGGSSHHAHPYAMSPSLGSLRPYPPGPAHLPPPHSQVSYSQAGPNGPPVSSSSNSSSSTSQGSYPCSHPSPSQGPQGAPYPFPPVPTVTTSSATLSTVIATVASSPAGYKTASPPGPPPYGKRAPSPGAYKTATPPGYKPGSPPSFRTGTPPGYRGTSPPAGPGTFKPGSPTVGPGPLPPAGPSGLPSLPPPPAAPASGPPLSATQIKQEPAEEYETPESPVPPARSPSPPPKVVDVPSHASQSARFNKHLDRGFNSCARSDLYFVPLEGSKLAKKRADLVEKVRREAEQRAREEKEREREREREKEREREKERELERSVKLAQEGRAPVECPSLGPVPHRPPFEPGSAVATVPPYLGPDTPALRTLSEYARPHVMSPGNRNHPFYVPLGAVDPGLLGYNVPALYSSDPAAREREREARERDLRDRLKPGFEVKPSELEPLHGVPGPGLDPFPRHGGLALQPGPPGLHPFPFHPSLGPLERERLALAAGPALRPDMSYAERLAAERQHAERVAALGNDPLARLQMLNVTPHHHQHSHIHSHLHLHQQDAIHAASASVHPLIDPLASGSHLTRIPYPAGTLPNPLLPHPLHENEVLRHQLFAAPYRDLPASLSAPMSAAHQLQAMHAQSAELQRLALEQQQWLHAHHPLHSVPLPAQEDYYSHLKKESDKPL B47603486C672637 andr_human Androgen receptor Dihydrotestosterone receptor Nuclear receptor subfamily 3 group C member 4 AR DHTR NR3C4 protein protein human Homo sapiens Human MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPGAAVAASKGLPQQLPAPPDEDDSAAPSTLSLLGPTFPGLSSCSADLKDILSEASTMQLLQQQQQEAVSEGSSSGRAREASGAPTSSKDNYLGGTSTISDNAKELCKAVSVSMGLGVEALEHLSPGEQLRGDCMYAPLLGVPPAVRPTPCAPLAECKGSLLDDSAGKSTEDTAEYSPFKGGYTKGLEGESLGCSGSAAAGSSGTLELPSTLSLYKSGALDEAAAYQSRDYYNFPLALAGPPPPPPPPHPHARIKLENPLDYGSAWAAAAAQCRYGDLASLHGAGAAGPGSGSPSAAASSSWHTLFTAEEGQLYGPCGGGGGGGGGGGGGGGGGGGGGGGEAGAVAPYGYTRPPQGLAGQESDFTAPDVWYPGGMVSRVPYPSPTCVKSEMGPWMDSYSGPYGDMRLETARDHVLPIDYYFPPQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGNLKLQEEGEASSTTSPTEETTQKLTVSHIEGYECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGKVKPIYFHTQ isolated polyq stretch_q35-becn1-1 2969264 N/A 2969268 unspecified role unspecified role bait bait purified purified K48_poly-ubiquitination ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 2969269 unspecified role unspecified role prey prey purified purified isolated polyq stretch_q35:p.Gln35[47] q81 poly-glutamine extension mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false c_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false 4A Beclin 1 K48-polyubiquitination was increased in cells expressing GFP–Q81 as compared to cells expressing GFP–Q35. becn1-atxn3-3 2969264 n/a 2969270 unspecified role unspecified role prey prey purified purified P54252-1:p.Gln296[19] q22_poly-glutamine_extension mutation mutation range range range range false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 2969268 unspecified role unspecified role bait bait purified purified physical association physical association false false false 4Bi Ataxin3Q28 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. becn1-atxn3-4 2969264 N/A 2969269 competitor competitor competitor unspecified role unspecified role n/a 2969270 unspecified role unspecified role prey prey purified purified P54252-1:p.Gln296[19] q22 poly-glutamine extension mutation mutation range range range range false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 2969268 unspecified role unspecified role bait bait purified purified physical association physical association false false false 4Bii Ataxin3Q28 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. becn1-atxn3-5 2969264 N/A 2969271 competitor competitor competitor unspecified role unspecified role n/a 2969270 unspecified role unspecified role prey prey purified purified P54252-1:p.Gln292_Gln305delinsGlnGlnGlnLysGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGln mutation mutation range range range range false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 2969268 unspecified role unspecified role bait bait purified purified physical association physical association false false false 4Biii Ataxin3Q28 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. becn1-htt-1 2969264 N/A 2969268 unspecified role unspecified role bait bait purified purified N/A 2969272 unspecified role unspecified role prey prey purified purified p.Gln35_Gln38del q17 poly-glutamine extension mutation mutation range range range range false c_terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false poly_Q_region required to bind necessary binding region required to bind range range range range false physical association physical association false false false Extended Data fig 7A A wild-type (Q17) huntingtin fragment (N-terminal 350 residues) bound to beclin 1, and this interaction was largely lost when the polyQ stretch was deleted. becn1-htt-2 2969264 N/A 2969268 unspecified role unspecified role bait bait purified purified n/a 2969270 unspecified role unspecified role prey prey P54252-1:p.Gln296[28] q28_poly-glutamine_extension[292..292-305..305 mutation mutation range range range range false n_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false association association false false false Extended Data fig 7B becn1-atxn3-6 2969264 N/A 2969272 competitor competitor competitor prey prey purified purified P42858:p.Gln18[138] mutation mutation range range range range false c_terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 2969268 unspecified role unspecified role bait bait purified purified n/a 2969270 unspecified role unspecified role prey prey P54252-1:p.Gln296[25] q28_poly-glutamine_extension mutation mutation range range range range false n_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false association association false false false Extended Data fig 7Bi becn1-atn1-1 2969264 N/A 2969268 unspecified role unspecified role bait bait purified purified K48_poly-ubiquitination ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 2969273 unspecified role unspecified role prey prey region egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false P54259:p.Gln484[71] mutation increasing strength mutation increasing interaction strength mutation increasing strength range range range range false n_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false association association false false false Extended Data fig 10A becn1-ar-1 2969264 N/A 2969268 unspecified role unspecified role bait bait purified purified K48_poly-ubiquitination ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 2969274 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false p.Gln88_Gln90del q25 poly-glutamine extension mutation mutation range range range range false n_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false P10275:p.Gln86[97] q120 poly-glutamine extension mutation increasing strength mutation increasing interaction strength mutation increasing strength range range range range false association association false false false Extended Data fig 10B The location of the Q25 and Q120 polyglutamine repeats is not known;there are three glutamine rich regions in AR. atxn3-becn1-2 2969265 N/A 2969268 unspecified role unspecified role prey prey purified purified c-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false n/a 2969270 unspecified role unspecified role bait bait purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P54252-1:p.Gln296[25] q28_poly-glutamine_extension mutation mutation range range range range false n_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 3A Ataxin3Q28 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. Deletion of the polyQ domain from ataxin 3 greatly reduced its binding to beclin 1 (Fig. 3a) atxn3-becn1-3 2969265 N/A 2969268 unspecified role unspecified role prey prey purified purified c-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 2969269 unspecified role unspecified role bait bait purified purified c_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false 3B Ataxin3Q28 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. Deletion of the polyQ domain from ataxin 3 greatly reduced its binding to beclin 1 (Fig. 3a) becn1-atxn3-1 2969265 N/A 2969268 unspecified role unspecified role bait bait purified purified c-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecd_region sufficient to bind sufficient binding region sufficient to bind range range range range false n/a 2969270 unspecified role unspecified role prey prey purified purified P54252-1:p.Gln296[25] q28_poly-glutamine_extension mutation mutation range range range range false n_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 3C Ataxin3Q28 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. becn1-atxn3-2 2969265 N/A 2969268 unspecified role unspecified role bait bait purified purified c-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecd_region sufficient to bind sufficient binding region sufficient to bind range range range range false not_the_ecd_region sufficient to bind sufficient binding region sufficient to bind range range range range false N/A 2969269 unspecified role unspecified role prey prey purified purified c_terminus egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false Extended Data 5A Ataxin3Q28 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. ataz-bec-1 2969266 n/a 2969270 unspecified role unspecified role bait bait N/A 2969268 unspecified role unspecified role prey prey physical association physical association false false false 2A atxn3-becn1-4 2969266 N/A 2969268 unspecified role unspecified role bait bait purified purified K48_poly-ubiquitination ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 2969270 unspecified role unspecified role prey prey purified purified P54252-1:p.Gln296[19] q22_poly-glutamine_extension' mutation mutation range range range range false n_terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false P54252-1:p.Gln296[77] q80 poly-glutamine extension mutation increasing strength mutation increasing interaction strength mutation increasing strength range range range range false physical association physical association false false false Extended Data fig 9D AT3Q22 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. Q80 mutant ataxin 3 interacted more strongly with beclin 1 than did wild-type ataxin 3, and this increased interaction was associated with increased beclin 1 K48 polyubiquitination. atxn3-becn1-1 2969267 N/A 2969268 enzyme target enzyme target substrate substrate neutral component neutral component purified purified HA-tagged ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false c-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 n/a 2969270 enzyme enzyme neutral component neutral component purified purified P54252-1:p.Gln296[19] q22_poly-glutamine_extension mutation mutation range range range range false P54252-1:p.Cys14Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false n_terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false P54252-1:p.Gln296[77] q80 poly-glutamine extension mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate range range range range false human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 deubiquitination deubiquitination reaction deubiquitination false false false 2B, Extended Data fig 9A AT3Q22 is a non-pathogenic form of ATX3 (In normal individuals, the ATXN3 gene was found to contain between 13 and 36 CAG repeats.) -from Omim. Expansion of the polyQ domain in ataxin 3 decreased its deubiquitinase activity towards beclin 1. P54252 (GO:0101005) up-regulates quantity by stabilization Q14457