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/ chuang-2007-2 SARA-regulated vesicular targeting underlies formation of the light-sensing organelle in mammalian rods. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Chuang JZ., Zhao Y., Sung CH. Synapse - Interactions of proteins with an established role in the presynapse. Source of STX3 inferred from previous work of contributer jzchuang@med.cornell.edu,chsung@med.cornell.edu izchuang@med.cornell.edu Bovine cDNA (no detail given in paper, inferred from species of interacting molecule). Cell (0092-8674) 2007 Only protein-protein interactions 7 imex curation chuang-2007-4 SARA-regulated vesicular targeting underlies formation of the light-sensing organelle in mammalian rods. 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. confocal microscopy confocal microscopy immunostaining immunostaining Chuang JZ., Zhao Y., Sung CH. Synapse - Interactions of proteins with an established role in the presynapse. Source of Stx-3 inferred from previous work of contributer jzchuang@med.cornell.edu,chsung@med.cornell.edu izchuang@med.cornell.edu Bovine cDNA (no detail given in paper, inferred from species of interacting molecule). Cell (0092-8674) 2007 Only protein-protein interactions 7 imex curation chuang-2007-1 SARA-regulated vesicular targeting underlies formation of the light-sensing organelle in mammalian rods. 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 nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Chuang JZ., Zhao Y., Sung CH. Synapse - Interactions of proteins with an established role in the presynapse. jzchuang@med.cornell.edu,chsung@med.cornell.edu izchuang@med.cornell.edu Bovine cDNA (no detail given in paper, inferred from species of interacting molecule). Cell (0092-8674) 2007 Only protein-protein interactions 7 imex curation chuang-2007-3 SARA-regulated vesicular targeting underlies formation of the light-sensing organelle in mammalian rods. mouse-retina Mus musculus retina retina retinal tissue anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Chuang JZ., Zhao Y., Sung CH. Synapse - Interactions of proteins with an established role in the presynapse. jzchuang@med.cornell.edu,chsung@med.cornell.edu izchuang@med.cornell.edu Bovine cDNA (no detail given in paper, inferred from species of interacting molecule). Cell (0092-8674) 2007 Only protein-protein interactions 7 imex curation chuang-2007-5 SARA-regulated vesicular targeting underlies formation of the light-sensing organelle in mammalian rods. 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 Chuang JZ., Zhao Y., Sung CH. Synapse - Interactions of proteins with an established role in the presynapse. Source of STX3 inferred from previous work of contributer jzchuang@med.cornell.edu,chsung@med.cornell.edu izchuang@med.cornell.edu Bovine cDNA (no detail given in paper, inferred from species of interacting molecule). Cell (0092-8674) 2007 Only protein-protein interactions 7 imex curation chuang-2007-6 SARA-regulated vesicular targeting underlies formation of the light-sensing organelle in mammalian rods. in vitro In vitro filter binding filter binding Filter overlay assay Filter overlay assay predetermined predetermined participant predetermined Chuang JZ., Zhao Y., Sung CH. Synapse - Interactions of proteins with an established role in the presynapse. jzchuang@med.cornell.edu,chsung@med.cornell.edu izchuang@med.cornell.edu Bovine cDNA (no detail given in paper, inferred from species of interacting molecule). Cell (0092-8674) 2007 Only protein-protein interactions 7 imex curation zfyv9_human Zinc finger FYVE domain-containing protein 9 ZFYVE9 MADHIP SARA SMADIP Mothers against decapentaplegic homolog-interacting protein Smad anchor for receptor activation Receptor activation anchor Novel serine protease protein protein human Homo sapiens Human MENYFQAEAYNLDKVLDEFEQNEDETVSSTLLDTKWNKILDPPSHRLSFNPTLASVNESAVSNESQPQLKVFSLAHSAPLTTEEEDHCANGQDCNLNPEIATMWIDENAVAEDQLIKRNYSWDDQCSAVEVGEKKCGNLACLPDEKNVLVVAVMHNCDKRTLQNDLQDCNNYNSQSLMDAFSCSLDNENRQTDQFSFSINESTEKDMNSEKQMDPLNRPKTEGRSVNHLCPTSSDSLASVCSPSQLKDDGSIGRDPSMSAITSLTVDSVISSQGTDGCPAVKKQENYIPDEDLTGKISSPRTDLGSPNSFSHMSEGILMKKEPAEESTTEESLRSGLPLLLKPDMPNGSGRNNDCERCSDCLVPNEVRADENEGYEHEETLGTTEFLNMTEHFSESQDMTNWKLTKLNEMNDSQVNEEKEKFLQISQPEDTNGDSGGQCVGLADAGLDLKGTCISESEECDFSTVIDTPAANYLSNGCDSYGMQDPGVSFVPKTLPSKEDSVTEEKEIEESKSECYSNIYEQRGNEATEGSGLLLNSTGDLMKKNYLHNFCSQVPSVLGQSSPKVVASLPSISVPFGGARPKQPSNLKLQIPKPLSDHLQNDFPANSGNNTKNKNDILGKAKLGENSATNVCSPSLGNISNVDTNGEHLESYEAEISTRPCLALAPDSPDNDLRAGQFGISARKPFTTLGEVAPVWVPDSQAPNCMKCEARFTFTKRRHHCRACGKVFCASCCSLKCKLLYMDRKEARVCVICHSVLMNAQAWENMMSASSQSPNPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGVLKHPGAEVAQPREQRRVWFADGILPNGEVADAAKLTMNGTSSAGTLAVSHDPVKPVTTSPLPAETDICLFSGSITQVGSPVGSAMNLIPEDGLPPILISTGVKGDYAVEEKPSQISVMQQLEDGGPDPLVFVLNANLLSMVKIVNYVNRKCWCFTTKGMHAVGQSEIVILLQCLPDEKCLPKDIFNHFVQLYRDALAGNVVSNLGHSFFSQSFLGSKEHGGFLYVTSTYQSLQDLVLPTPPYLFGILIQKWETPWAKVFPIRLMLRLGAEYRLYPCPLFSVRFRKPLFGETGHTIMNLLADFRNYQYTLPVVQGLVVDMEVRKTSIKIPSNRYNEMMKAMNKSNEHVLAGGACFNEKADSHLVCVQNDDGNYQTQAISIHNQPRKVTGASFFVFSGALKSSSGYLAKSSIVEDGVMVQITAENMDSLRQALREMKDFTITCGKADAEEPQEHIHIQWVDDDKNVSKGVVSPIDGKSMETITNVKIFHGSEYKANGKVIRWTEVFFLENDDQHNCLSDPADHSRLTEHVAKAFCLALCPHLKLLKEDGMTKLGLRVTLDSDQVGYQAGSNGQPLPSQYMNDLDSALVPVIHGGACQLSEGPVVMELIFYILENIV opsd_human Rhodopsin RHO OPN2 Opsin-2 protein protein human Homo sapiens Human MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA stx3_human Syntaxin-3 STX3 STX3A protein protein human Homo sapiens Human MKDRLEQLKAKQLTQDDDTDAVEIAIDNTAFMDEFFSEIEETRLNIDKISEHVEEAKKLYSIILSAPIPEPKTKDDLEQLTTEIKKRANNVRNKLKSMEKHIEEDEVRSSADLRIRKSQHSVLSRKFVEVMTKYNEAQVDFRERSKGRIQRQLEITGKKTTDEELEEMLESGNPAIFTSGIIDSQISKQALSEIEGRHKDIVRLESSIKELHDMFMDIAMLVENQGEMLDNIELNVMHTVDHVEKARDETKKAVKYQSQARKKLIIIIVLVVVLLGILALIIGLSVGLN eea1_human Early endosome antigen 1 EEA1 ZFYVE2 Endosome-associated protein p162 Zinc finger FYVE domain-containing protein 2 protein protein human Homo sapiens Human MLRRILQRTPGRVGSQGSDLDSSATPINTVDVNNESSSEGFICPQCMKSLGSADELFKHYEAVHDAGNDSGHGGESNLALKRDDVTLLRQEVQDLQASLKEEKWYSEELKKELEKYQGLQQQEAKPDGLVTDSSAELQSLEQQLEEAQTENFNIKQMKDLFEQKAAQLATEIADIKSKYDEERSLREAAEQKVTRLTEELNKEATVIQDLKTELLQRPGIEDVAVLKKELVQVQTLMDNMTLERERESEKLKDECKKLQSQYASSEATISQLRSELAKGPQEVAVYVQELQKLKSSVNELTQKNQTLTENLLKKEQDYTKLEEKHNEESVSKKNIQATLHQKDLDCQQLQSRLSASETSLHRIHVELSEKGEATQKLKEELSEVETKYQHLKAEFKQLQQQREEKEQHGLQLQSEINQLHSKLLETERQLGEAHGRLKEQRQLSSEKLMDKEQQVADLQLKLSRLEEQLKEKVTNSTELQHQLDKTKQQHQEQQALQQSTTAKLREAQNDLEQVLRQIGDKDQKIQNLEALLQKSKENISLLEKEREDLYAKIQAGEGETAVLNQLQEKNHTLQEQVTQLTEKLKNQSESHKQAQENLHDQVQEQKAHLRAAQDRVLSLETSVNELNSQLNESKEKVSQLDIQIKAKTELLLSAEAAKTAQRADLQNHLDTAQNALQDKQQELNKITTQLDQVTAKLQDKQEHCSQLESHLKEYKEKYLSLEQKTEELEGQIKKLEADSLEVKASKEQALQDLQQQRQLNTDLELRATELSKQLEMEKEIVSSTRLDLQKKSEALESIKQKLTKQEEEKKILKQDFETLSQETKIQHEELNNRIQTTVTELQKVKMEKEALMTELSTVKDKLSKVSDSLKNSKSEFEKENQKGKAAILDLEKTCKELKHQLQVQMENTLKEQKELKKSLEKEKEASHQLKLELNSMQEQLIQAQNTLKQNEKEEQQLQGNINELKQSSEQKKKQIEALQGELKIAVLQKTELENKLQQQLTQAAQELAAEKEKISVLQNNYEKSQETFKQLQSDFYGRESELLATRQDLKSVEEKLSLAQEDLISNRNQIGNQNKLIQELKTAKATLEQDSAKKEQQLQERCKALQDIQKEKSLKEKELVNEKSKLAEIEEIKCRQEKEITKLNEELKSHKLESIKEITNLKDAKQLLIQQKLELQGKADSLKAAVEQEKRNQQILKDQVKKEEEELKKEFIEKEAKLHSEIKEKEVGMKKHEENEAKLTMQITALNENLGTVKKEWQSSQRRVSELEKQTDDLRGEIAVLEATVQNNQDERRALLERCLKGEGEIEKLQTKVLELQRKLDNTTAAVQELGRENQSLQIKHTQALNRKWAEDNEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNALTPSSKKPVRVCDACFNDLQG f1mky4_bovin Zinc finger FYVE domain-containing protein ZFYVE9 protein protein bovin Bos taurus (Bovine) Bovine MENYFQAEAYNLDKVLDEFEQNEDETVSPILLDTKWNKILDPSSRQLSFNSALTSVNEPTVSESQPQLKVFSLAHSAPPDSEGEDHCANGQDCSLNPEINTMWIDENAVTEDQLIKRNCSRDDQCSTVEVGEKKCGNLACLPDEKNVLVVAVMHNCDKRTFQSDLQDCNNYNSQSLKNAFSCSLDNENRQTDQFSFSINGSTEKDMNSEKQMDPLNRPNAEGDSDKYICTTSDNLASVCSPSQLQDDENIDRDPSMSVITSLTLDSVISSQRTEEGPDVKQEDSTPDEVLTGKTSSPRTDLGSPNSFSHLSEEILMKKEPSEERTTEESTQSALPLLLKTDMPNGSGRDDNSEQVSDCLVPSEGKADDKEGCKHEEILGTKEFLNMTEHFSESQEMTNWKLTKPNKMNDSQVKKDNEKFLQMNQPEDTCDDSGECDRMAEAGLDLKGTCVNESEGCDFSTVMDTPAANSLSNCCDSYGMQSPVVCFVPKTLPSKEDSVTEEKEIEESKSECYSNIYEQRGNEATEGSGLLLNSTGDLTKKNYLHNFCSQVPSVLGQSSPKIVANLQSISVPFGGARPKQPSNLKLQIPKPLSDHLQNDLPANSGNTAKNKNDVLGKAKLGENSATNVCNASSGNISIADTNGDHLESYESGISSRPCLALAPESPDNDLRAGQFGISARKPFTTLGEVAPVWVPDSQAPNCMKCEARFTFTKRRHHCRACGKVFCASCCSLKCKLLYMDRKEARVCVICHSVLMNAQAWENMMSASSQSPNPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVGVLKHPGAEVAQPREQRRVWFADGILPNGEVADAAKLTMNGTSSAGTLAVAHDPVKPAATSPLPAETNISLFSGSITQVGSPVGSAMNLIPEDGLPPILISTGVKGDYAVEEKPSQISVMQQLEDGGPDPLVFVLNANLLSMVKIVNYVNRKCWCFTTKGMHAVGQSEIVILLQCLPDEKCLPKDIFNHFVQLYRDALAGNVVGNLGHSFFSQSFLGSKEHGGFLYVTSTYQSLQDLVLPTPPYLFGILIQKWETPWAKVFPIRLMLRLGAEYRLYPCPLFSVRFRKPLFGETGHTIMNLLADFRNYQYTLPVVQGLVVDMEVRKTSIKIPSNRYNEMIKAMNKSNEHVLAGGACFNEKADSHLVCVQNDDGNYQTQAISIHNQPRKVTGASFFVFSGALKSSSGYLAKSSIVEDGVMVQITAENMDALRQALREMKDFTITCGKAEAEDPQEQIHIQWVDDDKDVNKGVLSPIDGKSMESITSVKIFHGSEYKANGKVIRWTEVFFLENDDQHNCLSDPADHSRLTEHVAKAFCLALCPHLKLLKEDGMTKLGLRVTLDSDQVGYQAGSNGQPLPSQYMNDLDSALVPVIHGGACQLSEGPIVMELIFYILENIA Homologous to O95405 pi3p 1-phosphatidyl-1D-myo-inositol 3-phosphates small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) rho-zfyv9-2 Interaction between human Rhodopsin and ZFVY9 (SARA) identified by pulldown 665908 N/A 665914 unspecified role unspecified role prey prey region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 665915 unspecified role unspecified role bait bait c-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1E stx3-zfyv9-2 Interaction between STX3 and ZFVY9 (SARA) identified by pulldown 665908 N/A 665914 unspecified role unspecified role prey prey region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 665916 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false direct interaction direct interaction false false false Fig. 6C rho-zfyv9-4 Interaction between human Rhodopsin and ZFVY9 (SARA) identified by colocalization 665909 N/A 665915 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) N/A 665917 unspecified role unspecified role neutral component neutral component N/A 665914 unspecified role unspecified role neutral component neutral component 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 colocalization colocalization false false false 1G stx3-zfyv9-1 Interaction between STX3 and ZFVY9 (SARA) identified by colocalization 665909 N/A 665916 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 665914 unspecified role unspecified role neutral component neutral component 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 colocalization colocalization false false false Fig. 6B and Supp. Fig. 9 rho-zfyv9-1 Interaction between human Rhodopsin and bovine ZFVY9 (SARA) identified by Y2H 665910 N/A 665918 unspecified role unspecified role prey prey c-terminal sufficient to bind sufficient binding region sufficient to bind full dna sequence full identification by DNA sequencing full dna sequence undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 665915 unspecified role unspecified role bait bait c-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false The bovine SARA protein aligned to residues 729-1425 of the human protein 1C rho-zfyv9-3 Interaction between human Rhodopsin and ZFVY9 (SARA) identified by coimmunoprecipitation 665911 N/A 665915 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) N/A 665914 unspecified role unspecified role prey prey physical association physical association false false false 1F stx3-zfyv9-3 Interaction between STX3 and ZFVY9 (SARA) identified by coimmunoprecipitation 665912 N/A 665914 unspecified role unspecified role bait bait 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 665916 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 6D zfyv9-pi3p-1 Interaction between ZFYV9 and PI3P 665913 N/A 665914 unspecified role unspecified role prey prey N/A 665919 unspecified role unspecified role bait bait direct interaction direct interaction false false false Supp. Fig. 2