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/ bowen-2007-2 NKX3.1 homeodomain protein binds to topoisomerase I and enhances its activity. in vitro In vitro pull down pull down weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Bowen C., Stuart A., Ju JH., Tuan J., Blonder J., Conrads TP., Veenstra TD., Gelmann EP. Cancer - Interactions investigated in the context of cancer gelmanne@georgetown.edu Cancer Res. (0008-5472) 2007 Only protein-protein interactions imex curation bowen-2007-3 NKX3.1 homeodomain protein binds to topoisomerase I and enhances its activity. in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa predetermined predetermined participant predetermined Bowen C., Stuart A., Ju JH., Tuan J., Blonder J., Conrads TP., Veenstra TD., Gelmann EP. Cancer - Interactions investigated in the context of cancer Oligonucleotides were 5 end labeled with T4 polynucleotide kinase in the presence of gamma-[32P]ATP. gelmanne@georgetown.edu Cancer Res. (0008-5472) 2007 Only protein-protein interactions imex curation bowen-2007-5 NKX3.1 homeodomain protein binds to topoisomerase I and enhances its activity. human-lncap Human caucasian prostate carcinoma lncap Human caucasian prostate adenocarcinoma confocal microscopy confocal microscopy predetermined predetermined participant predetermined Bowen C., Stuart A., Ju JH., Tuan J., Blonder J., Conrads TP., Veenstra TD., Gelmann EP. Cancer - Interactions investigated in the context of cancer gelmanne@georgetown.edu Cancer Res. (0008-5472) 2007 Only protein-protein interactions imex curation bowen-2007-1 NKX3.1 homeodomain protein binds to topoisomerase I and enhances its activity. in vitro In vitro pull down pull down ms participant Identification by mass spectrometry ms participant Bowen C., Stuart A., Ju JH., Tuan J., Blonder J., Conrads TP., Veenstra TD., Gelmann EP. Cancer - Interactions investigated in the context of cancer gelmanne@georgetown.edu Cancer Res. (0008-5472) 2007 Only protein-protein interactions imex curation bowen-2007-4 NKX3.1 homeodomain protein binds to topoisomerase I and enhances its activity. human-lncap Human caucasian prostate carcinoma lncap Human caucasian prostate adenocarcinoma anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Bowen C., Stuart A., Ju JH., Tuan J., Blonder J., Conrads TP., Veenstra TD., Gelmann EP. Cancer - Interactions investigated in the context of cancer gelmanne@georgetown.edu Cancer Res. (0008-5472) 2007 Only protein-protein interactions imex curation nkx31_human Homeobox protein Nkx-3.1 Homeobox protein NK-3 homolog A NKX3-1 NKX3.1 NKX3A protein protein human Homo sapiens Human MLRVPEPRPGEAKAEGAAPPTPSKPLTSFLIQDILRDGAQRQGGRTSSQRQRDPEPEPEPEPEGGRSRAGAQNDQLSTGPRAAPEEAETLAETEPERHLGSYLLDSENTSGALPRLPQTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELGDLEKHSSLPALKEEAFSRASLVSVYNSYPYYPYLYCVGSWSPAFW top1_human DNA topoisomerase 1 DNA topoisomerase I TOP1 protein protein human Homo sapiens Human MSGDHLHNDSQIEADFRLNDSHKHKDKHKDREHRHKEHKKEKDREKSKHSNSEHKDSEKKHKEKEKTKHKDGSSEKHKDKHKDRDKEKRKEEKVRASGDAKIKKEKENGFSSPPQIKDEPEDDGYFVPPKEDIKPLKRPRDEDDADYKPKKIKTEDTKKEKKRKLEEEEDGKLKKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF topo1_bd_tetrahy_dna Tetrahymena 52-mer containing the Topoisomerase I binding site ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) TCTAGAGGATTTCGAAGACTTAGAGAAATTTCGAAGATCCCCGGGCGAGCTC nkx3_1_recog_seq NKX3.1 recognition sequence ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) GTATATAAGTAGTTG top1-nkx3_1 Topoisomerase I pulls down NKX3-1 in vitro 662216 N/A 662221 cofactor cofactor coenzyme prey prey region 35s radiolabel 35s radiolabel 35S s35 radiolabelled S35 s35 radiolabelled 35S S35 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false in vitro In vitro N/A 662222 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 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 2 A, 3 B Treatment with camptothecin, DNase or RNase did not affect this interaction. nkx3_1-top1-1 His-NKX3-1 pulls down topoisomerase I in vitro 662216 N/A 662222 cofactor cofactor coenzyme prey prey region 35s radiolabel 35s radiolabel 35S s35 radiolabelled S35 s35 radiolabelled 35S S35 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false in vitro In vitro N/A 662221 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 direct interaction direct interaction false false false 2 B topo1_bd-top1 Topo I binds a 50-mer containing the Topo I binding site 662217 N/A 662223 unspecified role unspecified role bait bait N/A 662222 unspecified role unspecified role prey prey region 35s radiolabel 35s radiolabel 35S s35 radiolabelled S35 s35 radiolabelled 35S S35 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false in vitro In vitro direct interaction direct interaction false false false 2 C NKX3.1 - the affinity of Top1 for the oligonucleotide appeared to increase in the presence of NKX3-1. nkx3_1_recog-nkx3_1 NKX3-1 binds the NKX3.1 recognition sequence 662217 N/A 662221 unspecified role unspecified role prey prey N/A 662224 unspecified role unspecified role bait bait direct interaction direct interaction false false false 2 D Topoisomerase I - this interaction only occurred in the presence topoisomerase I but at higher concentrations Topo I competes NKX3.1 from its cognate DNA sequence. nkx3_1-top1-3 Endogenous NKX3.1 and Topoisomerase I colocalize in LNCaP cells 662218 N/A 662222 unspecified role unspecified role neutral component neutral component N/A 662221 unspecified role unspecified role neutral component neutral component physical association physical association false false false Exposure to 20 Gy gamma-irradiation resulted in delocalization from the nuclear aggregates but continued colocalization of NKX3.1 and Topo I up to 45 min after irradiation. 9 A nkx3_1-top1-4 Endogenous NKX3.1 and EGFP-Topoisomerase I colocalize in LNCaP cells 662218 N/A 662221 unspecified role unspecified role neutral component neutral component N/A 662222 unspecified role unspecified role neutral component neutral component region EGFP tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false 9 B After exposure to mitomycin C, which generates double-stranded DNA breaks, both signals delocalized but remained nuclear and continued to colocalize to a substantial degree. nkx3_1-top1 NKX3-1 pulls down topoisomerase I from PC3 lysates 662219 N/A 662222 unspecified role unspecified role prey prey human-pc3 Human PC3 Caucasian prostate adenocarcinoma pc3 Human Caucasian prostate adenocarcinoma N/A 662221 unspecified role unspecified role bait bait region mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobb Escherichia coli (strain B / BL21) physical association physical association false false false 1 PC3 cells do not express endogenous NKX3-1. nkx3_1-top1-2 Endogenous NKX3.1 coimmunoprecipitates Topoisomerase I in LNCaP lysates 662220 N/A 662221 unspecified role unspecified role bait bait N/A 662222 unspecified role unspecified role prey prey physical association physical association false false false 8