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/ Quantitative characterization of Tob interactions provides the thermodynamic basis for translation termination-coupled deadenylase regulation. Quantitative characterization of Tob interactions provides the thermodynamic basis for translation termination-coupled deadenylase regulation. J. Biol. Chem. (0021-9258) 2010 imex curation Ruan L., Osawa M., Hosoda N., Imai S., Machiyama A., Katada T., Hoshino S., Shimada I. shimada@iw-nmr.f.u-tokyo.ac.jp 13-Jan-2014: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro nmr nuclear magnetic resonance NMR NMR nmr predetermined predetermined participant predetermined Ruan L., Osawa M., Hosoda N., Imai S., Machiyama A., Katada T., Hoshino S., Shimada I. shimada@ iw-nmr.f.u-tokyo.ac.jp shimada@iw-nmr.f.u-tokyo.ac.jp Accepted 2013-NOV-26 by PPORRAS J. Biol. Chem. (0021-9258) 2010 Only protein-protein interactions imex curation Quantitative characterization of Tob interactions provides the thermodynamic basis for translation termination-coupled deadenylase regulation. Quantitative characterization of Tob interactions provides the thermodynamic basis for translation termination-coupled deadenylase regulation. J. Biol. Chem. (0021-9258) 2010 imex curation Ruan L., Osawa M., Hosoda N., Imai S., Machiyama A., Katada T., Hoshino S., Shimada I. shimada@iw-nmr.f.u-tokyo.ac.jp 13-Jan-2014: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Ruan L., Osawa M., Hosoda N., Imai S., Machiyama A., Katada T., Hoshino S., Shimada I. shimada@ iw-nmr.f.u-tokyo.ac.jp shimada@iw-nmr.f.u-tokyo.ac.jp Accepted 2013-NOV-26 by PPORRAS J. Biol. Chem. (0021-9258) 2010 Only protein-protein interactions imex curation tob1_human Protein Tob1 Transducer of erbB-2 1 TOB1 TOB TROB1 protein protein human Homo sapiens Human MQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVDDNNENGCELDKEIKNSFNPEAQVFMPISDPASSVSSSPSPPFGHSAAVSPTFMPRSTQPLTFTTATFAATKFGSTKMKNSGRSNKVARTSPINLGLNVNDLLKQKAISSSMHSLYGLGLGSQQQPQQQQQPAQPPPPPPPPQQQQQQKTSALSPNAKEFIFPNMQGQGSSTNGMFPGDSPLNLSPLQYSNAFDVFAAYGGLNEKSFVDGLNFSLNNMQYSNQQFQPVMAN 3C8AC51B49E1E69F cnot7_human CCR4-NOT transcription complex subunit 7 CNOT7 CAF1 CCR4-associated factor 1 BTG1-binding factor 1 Caf1a protein protein human Homo sapiens Human MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAYEEEANKQS DIP protein Q9UIV1 original sequence version: 95 2AF23ED27E06EFDB pabp1_human Polyadenylate-binding protein 1 PABPC1 PAB1 PABP1 PABPC2 PABP protein protein human Homo sapiens Human MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSATGVPTV DIP protein P11940 original sequence version: 187 DIP protein P11940 original sequence version: 181 DIP protein P11940-1 original sequence version: 136 DIP protein P11940 original sequence version: 148 DIP protein P11940 original sequence version: 172 2EB1B02A346132EE cnot7-tob1-4 2 4 unspecified role unspecified role bait bait ecobd Escherichia coli (strain B / BL21-DE3) 3 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction Fig. 2, Table 1 Temp = 25C Kd values (molar) were measured for Tob1 peptides with different lengths: residues 1-285: 0.648 +/- 0.009 x 10E-6; residues 1-148: 0.59 +/- 0.03 x 10E-6. tob1-pabpc1 2 3 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) 5 unspecified role unspecified role prey prey pabp_hyd domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) 12 14 direct interaction direct interaction Fig. 3, Table 2 Temp = 25C; 50mM NaCl Kd was also determined in salt-free conditions (0mM NaCl) (with Tob residues 147-285): 8.03 +/- 0.01 x 10E-6 molar. No Kd could be determined under these conditions with Tob residues 1-148. pabpc1-tob1 2 5 unspecified role unspecified role bait bait pabp_hyd domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) 3 unspecified role unspecified role prey prey lig_pam2_1 motif sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain lig_pam2_1 motif sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction Table 2 Temp = 25C; 0mM NaCl Kd values were measured for different Tob peptides: residues 120-147: Kd = 57 +/- 4 x 10E-6 molar; residues 260-285: Kd = 9.3 +/- 0.3 x 10E-6 molar. pabpc1-tob1-1 1 3 unspecified role unspecified role neutral component neutral component region 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined lig_pam2_1 motif sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) 5 unspecified role unspecified role neutral component neutral component pabp_hyd domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) 24 26 direct interaction direct interaction Fig. 4 pabpc1-tob1-2 1 5 unspecified role unspecified role neutral component neutral component region 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined pabp_hyd domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) 3 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobd Escherichia coli (strain B / BL21-DE3) 30 32 direct interaction direct interaction Fig. 5