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/ orenstein-2013-1 Interplay of LRRK2 with chaperone-mediated autophagy. human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Orenstein S.J., Kuo S.H., Tasset I., Arias E., Koga H., Fernandez-Carasa I., Cortes E., Honig L.S., Dauer W., Consiglio A., Raya A., Sulzer D., Cuervo A.M. Parkinsons - Interactions investigated in the context of Parkinsons disease Figure 5C -Results from thes Pull down could not be included as the origin of GST-HSC70 is not given, neither were the authors willing to provide this information. ana-maria.cuervo@einstein.yu.edu,ds43@columbia.edu Nat. Neurosci. (1097-6256) 2013 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. orenstein-2013-2 Interplay of LRRK2 with chaperone-mediated autophagy. in vitro In vitro anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Orenstein S.J., Kuo S.H., Tasset I., Arias E., Koga H., Fernandez-Carasa I., Cortes E., Honig L.S., Dauer W., Consiglio A., Raya A., Sulzer D., Cuervo A.M. Parkinsons - Interactions investigated in the context of Parkinsons disease For both Figs 5F and 7C the cells used were stated only to be "lysosomes"; I have entered as Rat liver lysosomes from the context, however mouse brain lysosomes and neuronal lysosomes are used as well as Rat Liver lysosomes. Figure 5C -Results from thes Pull down could not be included as the origin of GST-HSC70 is not given, neither were the authors willing to provide this information. Rat liver lysosomes. ana-maria.cuervo@einstein.yu.edu,ds43@columbia.edu Nat. Neurosci. (1097-6256) 2013 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. orenstein-2013-4 Interplay of LRRK2 with chaperone-mediated autophagy. human-brain Homo sapiens brain brain Brain [cerebrum] confocal microscopy confocal microscopy immunohistochemistry immunohistochemistry Orenstein S.J., Kuo S.H., Tasset I., Arias E., Koga H., Fernandez-Carasa I., Cortes E., Honig L.S., Dauer W., Consiglio A., Raya A., Sulzer D., Cuervo A.M. Parkinsons - Interactions investigated in the context of Parkinsons disease Figure 5C -Results from thes Pull down could not be included as the origin of GST-HSC70 is not given, neither were the authors willing to provide this information. Sections from the dorsal motor nuclei of the vagus nerves of brains from two different unaffected control (Ctr) individuals and two individuals with Parkinson's disease with the G/S LRRK2 mutation. ana-maria.cuervo@einstein.yu.edu,ds43@columbia.edu Nat. Neurosci. (1097-6256) 2013 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. orenstein-2013-3 Interplay of LRRK2 with chaperone-mediated autophagy. human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. fluorescence imaging fluorescence microscopy fluorescence imaging immunohistochemistry immunohistochemistry Orenstein S.J., Kuo S.H., Tasset I., Arias E., Koga H., Fernandez-Carasa I., Cortes E., Honig L.S., Dauer W., Consiglio A., Raya A., Sulzer D., Cuervo A.M. Parkinsons - Interactions investigated in the context of Parkinsons disease Figure 5C -Results from thes Pull down could not be included as the origin of GST-HSC70 is not given, neither were the authors willing to provide this information. ana-maria.cuervo@einstein.yu.edu,ds43@columbia.edu Nat. Neurosci. (1097-6256) 2013 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. lrrk2_human Leucine-rich repeat serine/threonine-protein kinase 2 LRRK2 PARK8 Dardarin protein protein human Homo sapiens Human MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLGCKALHVLFERVSEEQLTEFVENKDYMILLSALTNFKDEEEIVLHVLHCLHSLAIPCNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNILVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEEDKLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSMLMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKMLNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTEFHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGAMDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQTKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMDDYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSGSREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDKTSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDSVFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDLLKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCCISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDVSRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSPLRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKFSCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWSRVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLNFDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEFPVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKIMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEEYLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRERALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHIDSLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQPRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE hsp7c_human Heat shock cognate 71 kDa protein HSPA8 HSC70 HSP73 HSPA10 Heat shock 70 kDa protein 8 Lipopolysaccharide-associated protein 1 protein protein human Homo sapiens Human MSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGGAPPSGGASSGPTIEEVD lamp2_human Lysosome-associated membrane glycoprotein 2 LAMP2 CD107 antigen-like family member B LGP-96 protein protein human Homo sapiens Human MVCFRLFPVPGSGLVLVCLVLGAVRSYALELNLTDSENATCLYAKWQMNFTVRYETTNKTYKTVTISDHGTVTYNGSICGDDQNGPKIAVQFGPGFSWIANFTKAASTYSIDSVSFSYNTGDNTTFPDAEDKGILTVDELLAIRIPLNDLFRCNSLSTLEKNDVVQHYWDVLVQAFVQNGTVSTNEFLCDKDKTSTVAPTIHTTVPSPTTTPTPKEKPEAGTYSVNNGNDTCLLATMGLQLNITQDKVASVININPNTTHSTGSCRSHTALLRLNSSTIKYLDFVFAVKNENRFYLKEVNISMYLVNGSVFSIANNNLSYWDAPLGSSYMCNKEQTVSVSGAFQINTFDLRVQPFNVTQGKYSTAQDCSADDDNFLVPIAVGAALAGVLILVLLAYFIGLKHHHAGYEQF lamp2_rat Lysosome-associated membrane glycoprotein 2 Lysosomal membrane glycoprotein type B LGP-96 LGP-110 CD107 antigen-like family member B Lamp2 Lamp-2 protein protein rat Rattus norvegicus (Rat) Rat MRLLSPVTGSKLVLLFLFLGAVRSDALKLNLTDSKGTCLYAEWEMNFTITYEALKVNETVTITVPDKVTYNGSSCGDDKNGAKIMIQYGSTLSWAVNFTKEASQYFINNITLSYNTNDTKTFPGAVPKGILTVIIPVGSQLPLGVIFKCSSVLTFNLSPVVQHYWGIHLQAFVQNGTVSKHEQVCKEDKTATTVAPIIHTTVPSPTTTLTPTSIPVPTPTVGNYTISNGNATCLLATMGLQLNITEEKVPFIFNINPAITNFTGSCQPQTAQLRLNNSQIKYLDFIFAVKNEKRFYLKEVNVNMYLANGSAFHVSNNNLSFWDAPLGSSYMCNKEQVVSVSRTFQINTFNLKVQPFNVTKGEYSTAQDCSADEDNFLVPIAVGAALGGVLILVLLAYFIGLKRHHTGYEQF lrrk2-hspa8 1377568 n/a 1377572 unspecified role unspecified role bait bait n_terminus 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 rck_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n/a 1377573 unspecified role unspecified role prey prey physical association physical association false false false 5D The absence of the CMA (chaperone-mediated autophagy) targeting motif M3 (QIRDK) markedly reduced the amount of hsc70 recovered. lrrk2-hspa8-1 1377568 n/a 1377572 unspecified role unspecified role bait bait n_terminus 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 roc_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n/a 1377573 unspecified role unspecified role prey prey physical association physical association false false false 5Di The absence of the CMA (chaperone-mediated autophagy) targeting motif M3 (QIRDK) in LRRK2 markedly reduced the amount of hsc70 recovered. lrrk2-lamp2-1 1377568 n/a 1377574 unspecified role unspecified role prey prey n/a 1377572 unspecified role unspecified role bait bait n_terminus 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 Q5S007:p.Gly2019Ser mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Arg1441Cys mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 7D lrrk2-lamp2 1377569 n/a 1377572 unspecified role unspecified role bait bait Q5S007:p.Gly2019Ser mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Arg1441Cys mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false n/a 1377575 unspecified role unspecified role prey prey rat-liver rattus norvegicus liver Rat liver liver physical association physical association false false false 5F, 7C lamp2-lrrk2 1377570 n/a 1377572 unspecified role unspecified role neutral component neutral component Q5S007:p.Gly2019Ser mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false n/a 1377574 unspecified role unspecified role neutral component neutral component colocalization colocalization false false false 6C, supp 7B The association of LRRK2 with LAMP-2A–positive compartments was also markedly increased in the brains of the Parkinson's disease patients. lamp2-lrrk2-1 1377571 n/a 1377573 unspecified role unspecified role neutral component neutral component n/a 1377574 unspecified role unspecified role neutral component neutral component colocalization colocalization false false false supp 6A Levels of LAMP-2A were about twice as high in cells expressing either WT or G/S LRRK2 as in control cells.