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/ yim-2009-3 Rak functions as a tumor suppressor by regulating PTEN protein stability and function. human-u2-os Human U2-OS osteosarcoma cell line u2-os U2-OS osteocaroma cell line Not in CAPRI and no primary literature reference anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Yim EK., Peng G., Dai H., Hu R., Li K., Lu Y., Mills GB., Meric-Bernstam F., Hennessy BT., Craven RJ., Lin SY. Apoptosis - Interactions involving proteins with a function related to apoptosis U2OS cells were transiently transfected with empty vector or FLAG-PTEN plasmids. Whole cellular extracts were immunoprecipitated with anti-FLAG M2 affinity gel. Bead-bound immunocomplexes were eluted with 3 � FLAG peptide and subjected to SDS-PAGE. Silver staining was performed with a SilverSNAP mass spectrometry kit. Specific bands were excised and digested, and the peptides were analyzed by mass spectrometry. Source of flag-pten supplied by author. sylin@mdanderson.org Cancer Cell (1535-6108) 2009 Only protein-protein interactions 11 imex curation Cancer - Interactions investigated in the context of cancer yim-2009-2 Rak functions as a tumor suppressor by regulating PTEN protein stability and function. human-u2-os Human U2-OS osteosarcoma cell line u2-os U2-OS osteocaroma cell line Not in CAPRI and no primary literature reference anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Yim EK., Peng G., Dai H., Hu R., Li K., Lu Y., Mills GB., Meric-Bernstam F., Hennessy BT., Craven RJ., Lin SY. Apoptosis - Interactions involving proteins with a function related to apoptosis U2OS cells were transiently transfected with empty vector or FLAG-PTEN plasmids. Whole cellular extracts were immunoprecipitated with anti-FLAG M2 affinity gel. Bead-bound immunocomplexes were eluted with 3 � FLAG peptide and subjected to SDS-PAGE. Silver staining was performed with a SilverSNAP mass spectrometry kit. Specific bands were excised and digested, and the peptides were analyzed by mass spectrometry. Source of flag-pten supplied by author. sylin@mdanderson.org Cancer Cell (1535-6108) 2009 Only protein-protein interactions 11 imex curation Cancer - Interactions investigated in the context of cancer yim-2009-4 Rak functions as a tumor suppressor by regulating PTEN protein stability and function. human-mcf10a Human non-transformed breast epithelial cell line mcf10a non-transformed human breast epithelial cell line anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Yim EK., Peng G., Dai H., Hu R., Li K., Lu Y., Mills GB., Meric-Bernstam F., Hennessy BT., Craven RJ., Lin SY. Apoptosis - Interactions involving proteins with a function related to apoptosis U2OS cells were transiently transfected with empty vector or FLAG-PTEN plasmids. Whole cellular extracts were immunoprecipitated with anti-FLAG M2 affinity gel. Bead-bound immunocomplexes were eluted with 3 � FLAG peptide and subjected to SDS-PAGE. Silver staining was performed with a SilverSNAP mass spectrometry kit. Specific bands were excised and digested, and the peptides were analyzed by mass spectrometry. Source of flag-pten supplied by author. sylin@mdanderson.org Cancer Cell (1535-6108) 2009 Only protein-protein interactions 11 imex curation Cancer - Interactions investigated in the context of cancer yim-2009-6 Rak functions as a tumor suppressor by regulating PTEN protein stability and function. in vitro In vitro protein kinase assay protein kinase assay weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Yim EK., Peng G., Dai H., Hu R., Li K., Lu Y., Mills GB., Meric-Bernstam F., Hennessy BT., Craven RJ., Lin SY. Apoptosis - Interactions involving proteins with a function related to apoptosis U2OS cells were transiently transfected with empty vector or FLAG-PTEN plasmids. Whole cellular extracts were immunoprecipitated with anti-FLAG M2 affinity gel. Bead-bound immunocomplexes were eluted with 3 � FLAG peptide and subjected to SDS-PAGE. Silver staining was performed with a SilverSNAP mass spectrometry kit. Specific bands were excised and digested, and the peptides were analyzed by mass spectrometry. Source of flag-pten supplied by author. sylin@mdanderson.org Cancer Cell (1535-6108) 2009 Only protein-protein interactions 11 imex curation Cancer - Interactions investigated in the context of cancer yim-2009-1 Rak functions as a tumor suppressor by regulating PTEN protein stability and function. human-u2-os Human U2-OS osteosarcoma cell line u2-os U2-OS osteocaroma cell line Not in CAPRI and no primary literature reference pull down pull down de novo protein sequence de novo protein sequencing by mass spectrometry de novo protein sequence Yim EK., Peng G., Dai H., Hu R., Li K., Lu Y., Mills GB., Meric-Bernstam F., Hennessy BT., Craven RJ., Lin SY. Apoptosis - Interactions involving proteins with a function related to apoptosis U2OS cells were transiently transfected with empty vector or FLAG-PTEN plasmids. Whole cellular extracts were immunoprecipitated with anti-FLAG M2 affinity gel. Bead-bound immunocomplexes were eluted with 3 � FLAG peptide and subjected to SDS-PAGE. Silver staining was performed with a SilverSNAP mass spectrometry kit. Specific bands were excised and digested, and the peptides were analyzed by mass spectrometry. Source of flag-pten supplied by author. sylin@mdanderson.org Cancer Cell (1535-6108) 2009 Only protein-protein interactions 11 imex curation Cancer - Interactions investigated in the context of cancer yim-2009-5 Rak functions as a tumor suppressor by regulating PTEN protein stability and function. human-mcf10a Human non-transformed breast epithelial cell line mcf10a non-transformed human breast epithelial cell line pull down pull down western blot western blot Immuno blot Immuno blot Yim EK., Peng G., Dai H., Hu R., Li K., Lu Y., Mills GB., Meric-Bernstam F., Hennessy BT., Craven RJ., Lin SY. Apoptosis - Interactions involving proteins with a function related to apoptosis U2OS cells were transiently transfected with empty vector or FLAG-PTEN plasmids. Whole cellular extracts were immunoprecipitated with anti-FLAG M2 affinity gel. Bead-bound immunocomplexes were eluted with 3 � FLAG peptide and subjected to SDS-PAGE. Silver staining was performed with a SilverSNAP mass spectrometry kit. Specific bands were excised and digested, and the peptides were analyzed by mass spectrometry. Source of flag-pten supplied by author. sylin@mdanderson.org Cancer Cell (1535-6108) 2009 Only protein-protein interactions 11 imex curation Cancer - Interactions investigated in the context of cancer pten_human Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN Phosphatase and tensin homolog Mutated in multiple advanced cancers 1 PTEN MMAC1 TEP1 protein protein human Homo sapiens Human MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV frk_human Tyrosine-protein kinase FRK PTK5 RAK FYN-related kinase Nuclear tyrosine protein kinase RAK FRK Protein-tyrosine kinase 5 protein protein human Homo sapiens Human MSNICQRLWEYLEPYLPCLSTEADKSTVIENPGALCSPQSQRHGHYFVALFDYQARTAEDLSFRAGDKLQVLDTLHEGWWFARHLEKRRDGSSQQLQGYIPSNYVAEDRSLQAEPWFFGAIGRSDAEKQLLYSENKTGSFLIRESESQKGEFSLSVLDGAVVKHYRIKRLDEGGFFLTRRRIFSTLNEFVSHYTKTSDGLCVKLGKPCLKIQVPAPFDLSYKTVDQWEIDRNSIQLLKRLGSGQFGEVWEGLWNNTTPVAVKTLKPGSMDPNDFLREAQIMKNLRHPKLIQLYAVCTLEDPIYIITELMRHGSLQEYLQNDTGSKIHLTQQVDMAAQVASGMAYLESRNYIHRDLAARNVLVGEHNIYKVADFGLARVFKVDNEDIYESRHEIKLPVKWTAPEAIRSNKFSIKSDVWSFGILLYEIITYGKMPYSGMTGAQVIQMLAQNYRLPQPSNCPQQFYNIMLECWNAEPKERPTFETLRWKLEDYFETDSSYSDANNFIR nedd4_human E3 ubiquitin-protein ligase NEDD4 Neural precursor cell expressed developmentally down-regulated protein 4 NEDD4 KIAA0093 NEDD4-1 Cell proliferation-inducing gene 53 protein PIG53 HECT-type E3 ubiquitin transferase NEDD4 protein protein human Homo sapiens Human MAQSLRLHFAARRSNTYPLSETSGDDLDSHVHMCFKRPTRISTSNVVQMKLTPRQTALAPLIKENVQSQERSSVPSSENVNKKSSCLQISLQPTRYSGYLQSSNVLADSDDASFTCILKDGIYSSAVVDNELNAVNDGHLVSSPAICSGSLSNFSTSDNGSYSSNGSDFGSCASITSGGSYTNSVISDSSSYTFPPSDDTFLGGNLPSDSTSNRSVPNRNTTPCEIFSRSTSTDPFVQDDLEHGLEIMKLPVSRNTKIPLKRYSSLVIFPRSPSTTRPTSPTSLCTLLSKGSYQTSHQFIISPSEIAHNEDGTSAKGFLSTAVNGLRLSKTICTPGEVRDIRPLHRKGSLQKKIVLSNNTPRQTVCEKSSEGYSCVSVHFTQRKAATLDCETTNGDCKPEMSEIKLNSDSEYIKLMHRTSACLPSSQNVDCQININGELERPHSQMNKNHGILRRSISLGGAYPNISCLSSLKHNCSKGGPSQLLIKFASGNEGKVDNLSRDSNRDCTNELSNSCKTRDDFLGQVDVPLYPLPTENPRLERPYTFKDFVLHPRSHKSRVKGYLRLKMTYLPKTSGSEDDNAEQAEELEPGWVVLDQPDAACHLQQQQEPSPLPPGWEERQDILGRTYYVNHESRRTQWKRPTPQDNLTDAENGNIQLQAQRAFTTRRQISEETESVDNRESSENWEIIREDEATMYSNQAFPSPPPSSNLDVPTHLAEELNARLTIFGNSAVSQPASSSNHSSRRGSLQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDERGRSYYVDHNSRTTTWTKPTVQATVETSQLTSSQSSAGPQSQASTSDSGQQVTQPSEIEQGFLPKGWEVRHAPNGRPFFIDHNTKTTTWEDPRLKIPAHLRGKTSLDTSNDLGPLPPGWEERTHTDGRIFYINHNIKRTQWEDPRLENVAITGPAVPYSRDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLWIEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFKFIGRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTELDLRFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEGFFELIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLMMDSEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLPPYESFEELWDKLQMAIENTQGFDGVD pten-frk-3 882544 n/a 882550 unspecified role unspecified role prey prey n/a 882551 unspecified role unspecified role bait bait sh3 region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis 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 physical association physical association false false false Fig 1C. The SH3 domain coodinates were inferred from the UniProt entry. pten-frk-4 882544 n/a 882551 unspecified role unspecified role prey prey n/a 882550 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 c2 domain sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false phosp_domain 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 Fig 1D. pten-nedd4 882544 n/a 882552 unspecified role unspecified role prey prey n/a 882550 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 P60484:p.Tyr336Phe 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 Fig 3F. pten-frk-1 882545 n/a 882551 unspecified role unspecified role prey prey n/a 882550 unspecified role unspecified role bait bait physical association physical association false false false Fig 1B. pten-frk-2 882545 n/a 882550 unspecified role unspecified role prey prey n/a 882551 unspecified role unspecified role bait bait physical association physical association false false false Fig 1B. pten-nedd 882546 n/a 882550 unspecified role unspecified role bait bait n/a 882552 unspecified role unspecified role prey prey physical association physical association false false false Fig 2D. The interaction between NEDD4 and PTEN is markedly increased in the absence of Rak. pten-nedd-1 882546 n/a 882550 unspecified role unspecified role prey prey n/a 882552 unspecified role unspecified role bait bait physical association physical association false false false Fig 2D. The interaction between NEDD4 and PTEN is markedly increased in the absence of Rak. pten-frk-6 882547 n/a 882551 enzyme enzyme 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 human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells n/a 882550 enzyme target enzyme target substrate substrate neutral component neutral component c terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecobb Escherichia coli (strain B / BL21) phosphorylation phosphorylation reaction phosphorylation false false false Fig 3A. pten-frk-7 882547 n/a 882550 enzyme target enzyme target substrate substrate 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 P60484:p.Tyr336Phe Alters kinetics of interaction mutation mutation certain certain sequence position certain certain certain sequence position certain false human-293t Homo sapiens 293 cells transformed with SV40 large T antigen 293t 293 cells expressing SV40 large T antigen. The original designation of this cell line was 293tsA1609neo. It is not in Cabri,ATCC or HyperCLDB. n/a 882551 enzyme enzyme neutral component neutral component P42685:p.Lys262Arg Alters kinetics of interaction mutation mutation 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 ecobd Escherichia coli (strain B / BL21-DE3) phosphorylation phosphorylation reaction phosphorylation false false false Fig 3C. pten-frk 882548 n/a 882551 unspecified role unspecified role prey prey n/a 882550 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 physical association physical association false false false Fig1A. pten-ubi-2 882549 n/a 882552 unspecified role unspecified role prey prey n/a 882550 unspecified role unspecified role bait bait 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 physical association physical association false false false Fig 2E.