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/ wu-2000-7 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Wu G., Chen YG., Ozdamar B., Gyuricza CA., Chong PA., Wrana JL., Massagué J., Shi Y. The current version of SARA in Uniprot (2020) has an extra 102 residues at the N-terminus as compared to the sequence in 2000. yshi@molbio.princeton.edu Science (New York, N.Y.) 2000 Only protein-protein interactions imex curation imex curation wu-2000-8 chlae-cos_1 Chlorocebus aethiops COS-1 cells Grivet cos_1 CV-1 Simian cells (cercopithecus aethiops) transformed by SV40 anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Wu G., Chen YG., Ozdamar B., Gyuricza CA., Chong PA., Wrana JL., Massagué J., Shi Y. The current version of SARA in Uniprot (2020) has an extra 102 residues at the N-terminus as compared to the sequence in 2000. yshi@molbio.princeton.edu Science (New York, N.Y.) 2000 Only protein-protein interactions imex curation imex curation wu-2000-9 in vitro In vitro affinity techniques affinity technology affinity techniques weight by staining molecular weight estimation by staining weight by staining Wu G., Chen YG., Ozdamar B., Gyuricza CA., Chong PA., Wrana JL., Massagué J., Shi Y. Purified Smad-binding fragment from SARA and the MH2 domain from Smad2 (residues 241-467) mixed and incubated. The complex was then passed through a cation-exchange column to which Smad2 MH2 domain binds avidly. GST-SARA SBD in isolation does not bind this column. The current version of SARA in Uniprot (2020) has an extra 102 residues at the N-terminus as compared to the sequence in 2000. yshi@molbio.princeton.edu Science (New York, N.Y.) 2000 Only protein-protein interactions imex curation imex curation wu-2000-10 chlae-cos_1 Chlorocebus aethiops COS-1 cells Grivet cos_1 CV-1 Simian cells (cercopithecus aethiops) transformed by SV40 confocal microscopy confocal microscopy anti tag immunost anti tag immunostaining anti tag immunost Wu G., Chen YG., Ozdamar B., Gyuricza CA., Chong PA., Wrana JL., Massagué J., Shi Y. The current version of SARA in Uniprot (2020) has an extra 102 residues at the N-terminus as compared to the sequence in 2000. yshi@molbio.princeton.edu Science (New York, N.Y.) 2000 Only protein-protein interactions imex curation imex curation smad2_human Mothers against decapentaplegic homolog 2 SMAD2 MADH2 MADR2 Mad-related protein 2 SMAD family member 2 JV18-1 protein protein human Homo sapiens Human MSSILPFTPPVVKRLLGWKKSAGGSGGAGGGEQNGQEEKWCEKAVKSLVKKLKKTGRLDELEKAITTQNCNTKCVTIPSTCSEIWGLSTPNTIDQWDTTGLYSFSEQTRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELKAIENCEYAFNLKKDEVCVNPYHYQRVETPVLPPVLVPRHTEILTELPPLDDYTHSIPENTNFPAGIEPQSNYIPETPPPGYISEDGETSDQQLNQSMDTGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS 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 smad2-zfyve9-1 3729758 N/A 3729762 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified MH2 domain binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 3729763 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified sbd domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Table 1 smad2-zfyve9-2 3729759 N/A 3729762 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed Q15796:p.Ser308_Glu309delinsAsnLys mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q15796:p.Gln294Ser mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q15796:p.Arg337His mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Q15796:p.Asn381Ser mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false FLAG tag FLAG tag 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 MH2 domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 3729763 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed MYC tag MYC tag myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Fig 1A smad2-zfyve9-3 3729760 N/A 3729762 unspecified role unspecified role bait bait purified purified n-terminus t7 tag t7 tag MASMTGGQQMG epitope tag MASMTGGQQMG epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false MH2 domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3729763 unspecified role unspecified role prey prey purified purified n-terminus 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 sbd domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false O95405:p.Tyr782Ala mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false O95405:p.Tyr782Glu mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false O95405:p.Cys783Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false O95405:p.Cys783Glu mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false O95405:p.Pro788Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false O95405:p.Pro788Glu mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false O95405:p.Gln790Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false O95405:p.Gln793Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false O95405:p.Val805Ala mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false O95405:p.Val805Glu mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig 1C zfyve9-smad2-2 3729761 N/A 3729762 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed Q15796:p.Asn381Ser mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false FLAG tag FLAG tag 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 3729763 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed MYC tag MYC tag myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false colocalization colocalization false false false 4B