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/ Regulation of STRA13 by the von Hippel-Lindau tumor suppressor protein, hypoxia, and the UBC9/ubiquitin proteasome degradation pathway. Regulation of STRA13 by the von Hippel-Lindau tumor suppressor protein, hypoxia, and the UBC9/ubiquitin proteasome degradation pathway. J. Biol. Chem. (0021-9258) 2001 imex curation Ivanova AV., Ivanov SV., Danilkovitch-Miagkova A., Lerman MI. Cancer - Interactions investigated in the context of cancer ivanova@mail.ncifcrf.gov 08-DEC-2006: Contacted by JYOTI. Returned mail. The cDNA human fetal kidney Matchmaker library (CLONTECH) was used. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast yeast display yeast display predetermined predetermined participant predetermined Ivanova AV., Ivanov SV., Danilkovitch-Miagkova A., Lerman MI. Cancer - Interactions investigated in the context of cancer ivanova@mail.ncifcrf.gov Accepted 2006-NOV-23 by DAVET. 08-DEC-2006: Contacted by JYOTI. Returned mail. J. Biol. Chem. (0021-9258) 2001 Only protein-protein interactions imex curation Regulation of STRA13 by the von Hippel-Lindau tumor suppressor protein, hypoxia, and the UBC9/ubiquitin proteasome degradation pathway. Regulation of STRA13 by the von Hippel-Lindau tumor suppressor protein, hypoxia, and the UBC9/ubiquitin proteasome degradation pathway. J. Biol. Chem. (0021-9258) 2001 imex curation Ivanova AV., Ivanov SV., Danilkovitch-Miagkova A., Lerman MI. Cancer - Interactions investigated in the context of cancer ivanova@mail.ncifcrf.gov 08-DEC-2006: Contacted by JYOTI. Returned mail. The cDNA human fetal kidney Matchmaker library (CLONTECH) was used. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Ivanova AV., Ivanov SV., Danilkovitch-Miagkova A., Lerman MI. Cancer - Interactions investigated in the context of cancer ivanova@mail.ncifcrf.gov Accepted 2006-NOV-24 by DAVET. 08-DEC-2006: Contacted by JYOTI. Returned mail. The cDNA human fetal kidney Matchmaker library (CLONTECH) was used. J. Biol. Chem. (0021-9258) 2001 Only protein-protein interactions imex curation Regulation of STRA13 by the von Hippel-Lindau tumor suppressor protein, hypoxia, and the UBC9/ubiquitin proteasome degradation pathway. Regulation of STRA13 by the von Hippel-Lindau tumor suppressor protein, hypoxia, and the UBC9/ubiquitin proteasome degradation pathway. J. Biol. Chem. (0021-9258) 2001 imex curation Ivanova AV., Ivanov SV., Danilkovitch-Miagkova A., Lerman MI. Cancer - Interactions investigated in the context of cancer ivanova@mail.ncifcrf.gov 08-DEC-2006: Contacted by JYOTI. Returned mail. The cDNA human fetal kidney Matchmaker library (CLONTECH) was used. Only protein-protein interactions 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 western blot western blot Immuno blot Immuno blot Ivanova AV., Ivanov SV., Danilkovitch-Miagkova A., Lerman MI. Cancer - Interactions investigated in the context of cancer ivanova@mail.ncifcrf.gov Accepted 2006-NOV-23 by DAVET. 08-DEC-2006: Contacted by JYOTI. Returned mail. J. Biol. Chem. (0021-9258) 2001 Only protein-protein interactions imex curation bhe40_human Class E basic helix-loop-helix protein 40 BHLHE40 Differentially expressed in chondrocytes protein 1 Enhancer-of-split and hairy-related protein 2 Stimulated by retinoic acid gene 13 protein BHLHB2 DEC1 SHARP2 STRA13 Class B basic helix-loop-helix protein 2 protein protein human Homo sapiens Human MERIPSAQPPPACLPKAPGLEHGDLPGMYPAHMYQVYKSRRGIKRSEDSKETYKLPHRLIEKKRRDRINECIAQLKDLLPEHLKLTTLGHLEKAVVLELTLKHVKALTNLIDQQQQKIIALQSGLQAGELSGRNVETGQEMFCSGFQTCAREVLQYLAKHENTRDLKSSQLVTHLHRVVSELLQGGTSRKPSDPAPKVMDFKEKPSSPAKGSEGPGKNCVPVIQRTFAHSSGEQSGSDTDTDSGYGGESEKGDLRSEQPCFKSDHGRRFTMGERIGAIKQESEEPPTKKNRMQLSDDEGHFTSSDLISSPFLGPHPHQPPFCLPFYLIPPSATAYLPMLEKCWYPTSVPVLYPGLNASAAALSSFMNPDKISAPLLMPQRLPSPLPAHPSVDSSVLLQALKPIPPLNLETKD DIP protein O14503 original sequence version: 112 2D73A3D4980793E5 ubc9_human SUMO-conjugating enzyme UBC9 UBE2I p18 SUMO-protein ligase UBC9 UBCE9 Ubiquitin carrier protein 9 Ubiquitin carrier protein I Ubiquitin-conjugating enzyme E2 I Ubiquitin-protein ligase I RING-type E3 SUMO transferase UBC9 protein protein human Homo sapiens Human MSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS DIP protein P63279 original sequence version: 33 DIP protein P63279 original sequence version: 57 DIP protein P63279 original sequence version: 80 DIP protein P63279 original sequence version: 137 DIP protein P63279 original sequence version: 99 DIP protein P63279 original sequence version: 140 DIP protein P63279 original sequence version: 120 DIP protein P63279 original sequence version: 117 DIP protein P63279 original sequence version: 93 E2C826E9C8D0683D bhlbh2-ube2i 2 5 unspecified role unspecified role prey prey 4 unspecified role unspecified role bait bait physical association physical association The authors state that full-length STRA13 is 411 residues long in the method for the yeast two hybrid experiment whereas the Uniprot entry is 412 residues (including the initial Met). Note in Fig. 3 STRA13 is represented as a 412 residue protein. To study the mechanisms of STRA13 regulation on protein level we searched for STRA13-binding partners using a yeast two-hybrid system. Out of 186 confirmed positive clones, five represented the entire cDNA (1.1 kilobase pair) of the UBC9 (human ubiquitin-conjugating enzyme) gene. bhlbh2-ube2i-1 1 4 unspecified role unspecified role bait bait 5 unspecified role unspecified role prey prey physical association physical association The authors state that full-length STRA13 is 411 residues long in the method for the yeast two hybrid experiment whereas the Uniprot entry is 412 residues (including the initial Met). Note in Fig. 3 STRA13 is represented as a 412 residue protein. Retransformation assay showed that GAL4-AD-UBC9 fusion protein interacted with pSTRA13 specifically, since no binding of ADUBC9 was detected with either the pAS2�1 vector alone (BD domain) or with pAS2�1-ARNT1 that produces the BD-ARNT1 fusion protein bhlbh2-ube2i-2 3 4 unspecified role unspecified role bait bait c-terminal required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain 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 5 unspecified role unspecified role prey prey physical association physical association The authors state that full-length STRA13 is 411 residues long in the method for the yeast two hybrid experiment whereas the Uniprot entry is 412 residues (including the initial Met). Note in Fig. 3 STRA13 is represented as a 412 residue protein. 3 The deletion of the C-terminal part of the STRA13 in the 1�299 mutant abolished the pSTRA13/pUBC9 interaction (Fig. 3B, line 7). Subsequent deletions of the N-terminal bHLH domain or three adjacent a-helices (Fig. 3, lines 3�6 and 8) did not lead to binding abrogation. Therefore, the region between amino acid residues 299 and 412 is absolutely required for the pSTRA13/pUBC9 interaction, whereas the bHLH domain and all three a-helices were dispensable.