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/ sasai-2008-1 Ectodermal factor restricts mesoderm differentiation by inhibiting p53. 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 anti tag western anti tag western blot anti tag western Sasai N., Yakura R., Kamiya D., Nakazawa Y., Sasai Y. Apoptosis - Interactions involving proteins with a function related to apoptosis norisa@cdb.riken.jp Cell (0092-8674) 2008 Only protein-protein interactions 4 imex curation sasai-2008-2 Ectodermal factor restricts mesoderm differentiation by inhibiting p53. xenla-animal_cap Xenopus laevis animal cap animal_cap Animal cap Xenopus laevis animal cap cells are cells situated around the animal (pigmented) pole of a blastula or very early gastrula-stage embryo. This tissue is fated to become cement gland/neurectoderm on the dorsal side of the embryo and epidermis on the ventral side. Animal caps are composed of pluripotent cells that can be induced to form endodermal, mesodermal, or ectodermal cell types. XAO:0000036. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Sasai N., Yakura R., Kamiya D., Nakazawa Y., Sasai Y. Apoptosis - Interactions involving proteins with a function related to apoptosis norisa@cdb.riken.jp Cell (0092-8674) 2008 Only protein-protein interactions 4 imex curation sasai-2008-3 Ectodermal factor restricts mesoderm differentiation by inhibiting p53. in vitro In vitro pull down pull down weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Sasai N., Yakura R., Kamiya D., Nakazawa Y., Sasai Y. Apoptosis - Interactions involving proteins with a function related to apoptosis norisa@cdb.riken.jp Cell (0092-8674) 2008 Only protein-protein interactions 4 imex curation sasai-2008-4 Ectodermal factor restricts mesoderm differentiation by inhibiting p53. in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift anti tag western anti tag western blot anti tag western Sasai N., Yakura R., Kamiya D., Nakazawa Y., Sasai Y. Apoptosis - Interactions involving proteins with a function related to apoptosis norisa@cdb.riken.jp Cell (0092-8674) 2008 Only protein-protein interactions 4 imex curation sasai-2008-5 Ectodermal factor restricts mesoderm differentiation by inhibiting p53. xenla-animal_cap Xenopus laevis animal cap animal_cap Animal cap Xenopus laevis animal cap cells are cells situated around the animal (pigmented) pole of a blastula or very early gastrula-stage embryo. This tissue is fated to become cement gland/neurectoderm on the dorsal side of the embryo and epidermis on the ventral side. Animal caps are composed of pluripotent cells that can be induced to form endodermal, mesodermal, or ectodermal cell types. XAO:0000036. ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Sasai N., Yakura R., Kamiya D., Nakazawa Y., Sasai Y. Apoptosis - Interactions involving proteins with a function related to apoptosis norisa@cdb.riken.jp Cell (0092-8674) 2008 Only protein-protein interactions 4 imex curation q9pst7_xenla znf585b.S znf585b protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MMHLIRNWPEKEKQNLNGSEMSRMKKIIEVGSERENIWGNLSQTQTHKESYRTPNQNYTSPMPQEYSYNGKLFALQREKLHNTNVQVIRMPNIAKQPKFNREIRSDSPKRKKAKSSEKSHVANISHQGTKINKFSKAQSALKSFICPICKRRFCNARNLLTHQRIHTGRRFVCSKCGKCFSNKKILIAHRWLHTGRKPFTCTKCNKGFLWNRDLQKHEKSHKEMRNKSLGLVHRHDKLREVSTDPCKREKSFDCTECGKSFKRKSKLKTHFLCHTGEKPFVCVHCGKGFRDNYKLSLHLRIHTGENLSVCPDCGKSYTDKNKLIVHMRIHTGEKFMCSECGKGFSDFYNLKSHLQIHTGEKPFVCPECGKSFLSKYEFKSHLLIHTGKYPFICSECGKSFMDKRYLKIHSNVHSGNTFPCTECGKSFAAKQNLKRHQKIHTGEKPHKCTECGKQFLQKNKLDRHHLSHTGVKPFSCFECGEQFTWKHLLQYHQLSHTGERPFVCSECGKGYKTKASLALHCHIHTGEKPFVCPECGNSYRSNGALRYHLQTHIKGKYFAHSEHGESDKSETNE p53_human Cellular tumor antigen p53 TP53 P53 Tumor suppressor p53 Phosphoprotein p53 Antigen NY-CO-13 protein protein human Homo sapiens Human MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD p53_xenla Cellular tumor antigen p53 Tumor suppressor p53 tp53 protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MEPSSETGMDPPLSQETFEDLWSLLPDPLQTVTCRLDNLSEFPDYPLAADMTVLQEGLMGNAVPTVTSCAVPSTDDYAGKYGLQLDFQQNGTAKSVTCTYSPELNKLFCQLAKTCPLLVRVESPPPRGSILRATAVYKKSEHVAEVVKRCPHHERSVEPGEDAAPPSHLMRVEGNLQAYYMEDVNSGRHSVCVPYEGPQVGTECTTVLYNYMCNSSCMGGMNRRPILTIITLETPQGLLLGRRCFEVRVCACPGRDRRTEEDNYTKKRGLKPSGKRELAHPPSSEPPLPKKRLVVVDDDEEIFTLRIKGRSRYEMIKKLNDALELQESLDQQKVTIKCRKCRDEIKPKKGKKLLVKDEQPDSE p53_be_human_dna Human p53 Binding Element DNA oligonucleotide ds dna double stranded deoxyribonucleic acid ds DNA ds dna human Homo sapiens Human TTTAGTCCTGTAGGCCAGGTCTGAGCCTGCACATCCCAGACAAG mix_2_xenla_gene Xenopus laevis Mix.2 promoter DNA sequence gene gene xenla Xenopus laevis (African clawed frog) African clawed frog tp53-xfdl Human TP53 coimmunoprecipitates XFDL 156 from HEK293 lysates 740997 N/A 741002 unspecified role unspecified role prey prey 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 741003 unspecified role unspecified role bait bait region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false P04637:p.[Lys370Gln;Lys372Gln;Lys373Gln;Lys381Gln;Lys382Gln] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P04637:p.[Lys370Arg;Lys372Arg;Lys373Arg;Lys381Arg;Lys382Arg] mutation increasing mutation increasing interaction mutation increasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P04637:p.[Lys373Arg;Lys382Arg] mutation increasing mutation increasing interaction mutation increasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P04637:p.[Lys373Gln;Lys382Gln] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false n-terminal hp53DeltaRD 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 5 A, 6 A, 6 G, S4 D P04637; Q9PST7 transfection tp53-xfdl-3 Human TP53 coimmunoprecipitates XFDL 156 from HEK293 lysates 740997 N/A 741002 unspecified role unspecified role prey prey 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 741003 unspecified role unspecified role bait bait n-terminal Venus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain range range false physical association physical association false false false S4 B, D The end of the tp53 range is given as fuzzy coordinates as it is not clear from Fig. S4 A exactly where the end of the construct is. The last two, (the 13th and 14th), Zn-finger motifs were necessary and sufficient for binding to p53. However, the authors did not give the range for this construct. tp53-xfdl-1 Xenopus tp53 coimmunoprecipitates XFDL 156 from Xenopus animal cap extracts 740998 N/A 741002 unspecified role unspecified role prey prey N/A 741004 unspecified role unspecified role bait bait region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false 5 B P07193 injection tp53-xfdl-2 Human TP53 pulls down XFDL 156 in vitro 740999 N/A 741003 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 N/A 741002 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 5 C It was not possible to determine what cell type was used to express the GST-tp53. p53_be_human-tp53 TP53 bound to the p53 binding element in an EMSA assay 741000 N/A 741003 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false P04637:p.[Lys373Gln;Lys382Gln] mutation increasing mutation increasing interaction mutation increasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false xenla-animal_cap Xenopus laevis animal cap animal_cap Animal cap Xenopus laevis animal cap cells are cells situated around the animal (pigmented) pole of a blastula or very early gastrula-stage embryo. This tissue is fated to become cement gland/neurectoderm on the dorsal side of the embryo and epidermis on the ventral side. Animal caps are composed of pluripotent cells that can be induced to form endodermal, mesodermal, or ectodermal cell types. XAO:0000036. N/A 741005 unspecified role unspecified role bait bait physical association physical association false false false 5 D The constitutively active TP53 mutant (K373Q/K382Q) efficiently bound the probe, whereas wild-type TP53 did not bind the probe at high levels. Injection of XFDL-MO (Morpholino antisense oligonucleotide to XFDL156) substantially enhanced binding of wild-type TP53 to the probe. This indicates that endogenous XFDL in the animal cap inhibits wild-type TP53 binding to the TP53 binding element. tp53-mix_2 TP53 binds the Mix.2 promoter in Xenopus animal caps 741001 N/A 741006 unspecified role unspecified role prey prey N/A 741004 unspecified role unspecified role bait bait association association false false false 5 E Binding of p53 to the Mix.2 promoter was enhanced by coinjection of XFDL-MO (Morpholino antisense oligonucleotides to XFDL) and suppressed by XFDL overexpression. Binding to the promoter of the Mix 2 gene was assayed.