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/ soehn-2010-1 Periphilin is a novel interactor of synphilin-1, a protein implicated in Parkinson's disease. 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 Soehn A.S., Franck T., Biskup S., Giaime E., Melle C., Rott R., Cebo D., Kalbacher H., Ott E., Pahnke J., Meitinger T., Krüger R., Gasser T., Berg D., von Eggeling F., Engelender S., da Costa C.A., Riess O. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. The Periphilin isoform (brain) of 313 amino acids-as used throughout this paper, does not currently appear to have a UniProt (or NCBI) identifier. The authors states:- "The periphilin isoform studied in this work lacks exons 1, 2, 4, and 12–14 (exon 1 as part of the 5′UTR, the remaining exons due to alternative splicing) and is, therefore, identical to the keratinocyte-specific isoform described before [14]. AND "The coding sequence (CDS) has a total length of 939 base pairs encoding 313 aa..." Thus an (INTERNAL) protein entry has been created to represent this Brain isoform of Periphilin, using the exon 3 transcript (from the second ATG corresponding to amino acids 1-24 from Isoform 1) and amino acids 87-374 from entry GenBank: AAO16497.1 - from Reference 14, (corresponding 99% to Isoform-6 amino acids 32-319- with one mismatch). This results in a 312 amino acid protein that has a lysine at position 69 - which gives the correct mutation mapping for the stated K69E mutation. The human Synphilin-1 protein has been assumed to have a maximum length of 919 amino acids, despite a "920" amino acid construct being used. anne.soehn@med.uni-tuebingen.de Human brain complementary DNA Neurogenetics (1364-6745) 2010 Only protein-protein interactions imex curation Parkinsons - Interactions investigated in the context of Parkinsons disease soehn-2010-2 Periphilin is a novel interactor of synphilin-1, a protein implicated in Parkinson's disease. 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 predetermined predetermined participant predetermined Soehn A.S., Franck T., Biskup S., Giaime E., Melle C., Rott R., Cebo D., Kalbacher H., Ott E., Pahnke J., Meitinger T., Krüger R., Gasser T., Berg D., von Eggeling F., Engelender S., da Costa C.A., Riess O. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. The Periphilin isoform (brain) of 313 amino acids-as used throughout this paper, does not currently appear to have a UniProt (or NCBI) identifier. The authors states:- "The periphilin isoform studied in this work lacks exons 1, 2, 4, and 12–14 (exon 1 as part of the 5′UTR, the remaining exons due to alternative splicing) and is, therefore, identical to the keratinocyte-specific isoform described before [14]. AND "The coding sequence (CDS) has a total length of 939 base pairs encoding 313 aa..." Thus an (INTERNAL) protein entry has been created to represent this Brain isoform of Periphilin, using the exon 3 transcript (from the second ATG corresponding to amino acids 1-24 from Isoform 1) and amino acids 87-374 from entry GenBank: AAO16497.1 - from Reference 14, (corresponding 99% to Isoform-6 amino acids 32-319- with one mismatch). This results in a 312 amino acid protein that has a lysine at position 69 - which gives the correct mutation mapping for the stated K69E mutation. The human Synphilin-1 protein has been assumed to have a maximum length of 919 amino acids, despite a "920" amino acid construct being used. anne.soehn@med.uni-tuebingen.de Neurogenetics (1364-6745) 2010 Only protein-protein interactions imex curation Parkinsons - Interactions investigated in the context of Parkinsons disease soehn-2010-3 Periphilin is a novel interactor of synphilin-1, a protein implicated in Parkinson's disease. mouse-brain-cortex Mus musculus brain cortex brain_cortex Brain cortex [Cerebral cortex; Cerebrum cortex; Cortex; Pallium] anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Soehn A.S., Franck T., Biskup S., Giaime E., Melle C., Rott R., Cebo D., Kalbacher H., Ott E., Pahnke J., Meitinger T., Krüger R., Gasser T., Berg D., von Eggeling F., Engelender S., da Costa C.A., Riess O. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. The Periphilin isoform (brain) of 313 amino acids-as used throughout this paper, does not currently appear to have a UniProt (or NCBI) identifier. The authors states:- "The periphilin isoform studied in this work lacks exons 1, 2, 4, and 12–14 (exon 1 as part of the 5′UTR, the remaining exons due to alternative splicing) and is, therefore, identical to the keratinocyte-specific isoform described before [14]. AND "The coding sequence (CDS) has a total length of 939 base pairs encoding 313 aa..." Thus an (INTERNAL) protein entry has been created to represent this Brain isoform of Periphilin, using the exon 3 transcript (from the second ATG corresponding to amino acids 1-24 from Isoform 1) and amino acids 87-374 from entry GenBank: AAO16497.1 - from Reference 14, (corresponding 99% to Isoform-6 amino acids 32-319- with one mismatch). This results in a 312 amino acid protein that has a lysine at position 69 - which gives the correct mutation mapping for the stated K69E mutation. The human Synphilin-1 protein has been assumed to have a maximum length of 919 amino acids, despite a "920" amino acid construct being used. anne.soehn@med.uni-tuebingen.de Neurogenetics (1364-6745) 2010 Only protein-protein interactions imex curation Parkinsons - Interactions investigated in the context of Parkinsons disease soehn-2010-4 Periphilin is a novel interactor of synphilin-1, a protein implicated in Parkinson's disease. 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. confocal microscopy confocal microscopy immunocytochemistry immunocytochemistry Soehn A.S., Franck T., Biskup S., Giaime E., Melle C., Rott R., Cebo D., Kalbacher H., Ott E., Pahnke J., Meitinger T., Krüger R., Gasser T., Berg D., von Eggeling F., Engelender S., da Costa C.A., Riess O. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. The Periphilin isoform (brain) of 313 amino acids-as used throughout this paper, does not currently appear to have a UniProt (or NCBI) identifier. The authors states:- "The periphilin isoform studied in this work lacks exons 1, 2, 4, and 12–14 (exon 1 as part of the 5′UTR, the remaining exons due to alternative splicing) and is, therefore, identical to the keratinocyte-specific isoform described before [14]. AND "The coding sequence (CDS) has a total length of 939 base pairs encoding 313 aa..." Thus an (INTERNAL) protein entry has been created to represent this Brain isoform of Periphilin, using the exon 3 transcript (from the second ATG corresponding to amino acids 1-24 from Isoform 1) and amino acids 87-374 from entry GenBank: AAO16497.1 - from Reference 14, (corresponding 99% to Isoform-6 amino acids 32-319- with one mismatch). This results in a 312 amino acid protein that has a lysine at position 69 - which gives the correct mutation mapping for the stated K69E mutation. The human Synphilin-1 protein has been assumed to have a maximum length of 919 amino acids, despite a "920" amino acid construct being used. anne.soehn@med.uni-tuebingen.de Neurogenetics (1364-6745) 2010 Only protein-protein interactions imex curation Parkinsons - Interactions investigated in the context of Parkinsons disease soehn-2010-6 Periphilin is a novel interactor of synphilin-1, a protein implicated in Parkinson's disease. 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. immunodepletion immunodepleted coimmunoprecipitation immunodepleted coip immunodepletion ms participant Identification by mass spectrometry ms participant Soehn A.S., Franck T., Biskup S., Giaime E., Melle C., Rott R., Cebo D., Kalbacher H., Ott E., Pahnke J., Meitinger T., Krüger R., Gasser T., Berg D., von Eggeling F., Engelender S., da Costa C.A., Riess O. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. The Periphilin isoform (brain) of 313 amino acids-as used throughout this paper, does not currently appear to have a UniProt (or NCBI) identifier. The authors states:- "The periphilin isoform studied in this work lacks exons 1, 2, 4, and 12–14 (exon 1 as part of the 5′UTR, the remaining exons due to alternative splicing) and is, therefore, identical to the keratinocyte-specific isoform described before [14]. AND "The coding sequence (CDS) has a total length of 939 base pairs encoding 313 aa..." Thus an (INTERNAL) protein entry has been created to represent this Brain isoform of Periphilin, using the exon 3 transcript (from the second ATG corresponding to amino acids 1-24 from Isoform 1) and amino acids 87-374 from entry GenBank: AAO16497.1 - from Reference 14, (corresponding 99% to Isoform-6 amino acids 32-319- with one mismatch). This results in a 312 amino acid protein that has a lysine at position 69 - which gives the correct mutation mapping for the stated K69E mutation. The human Synphilin-1 protein has been assumed to have a maximum length of 919 amino acids, despite a "920" amino acid construct being used. anne.soehn@med.uni-tuebingen.de Neurogenetics (1364-6745) 2010 Only protein-protein interactions imex curation Parkinsons - Interactions investigated in the context of Parkinsons disease sncap_human Synphilin-1 Alpha-synuclein-interacting protein SNCAIP protein protein human Homo sapiens Human MEAPEYLDLDEIDFSDDISYSVTSLKTIPELCRRCDTQNEDRSVSSSSWNCGISTLITNTQKPTGIADVYSKFRPVKRVSPLKHQPETLENNESDDQKNQKVVEYQKGGESDLGPQPQELGPGDGVGGPPGKSSEPSTSLGELEHYDLDMDEILDVPYIKSSQQLASFTKVTSEKRILGLCTTINGLSGKACSTGSSESSSSNMAPFCVLSPVKSPHLRKASAVIHDQHKLSTEETEISPPLVKCGSAYEPENQSKDFLNKTFSDPHGRKVEKTTPDCQLRAFHLQSSAAESKPEEQVSGLNRTSSQGPEERSEYLKKVKSILNIVKEGQISLLPHLAADNLDKIHDENGNNLLHIAASQGHAECLQHLTSLMGEDCLNERNTEKLTPAGLAIKNGQLECVRWMVSETEAIAELSCSKDFPSLIHYAGCYGQEKILLWLLQFMQEQGISLDEVDQDGNSAVHVASQHGYLGCIQTLVEYGANVTMQNHAGEKPSQSAERQGHTLCSRYLVVVETCMSLASQVVKLTKQLKEQTVERVTLQNQLQQFLEAQKSEGKSLPSSPSSPSSPASRKSQWKSPDADDDSVAKSKPGVQEGIQVLGSLSASSRARPKAKDEDSDKILRQLLGKEISENVCTQEKLSLEFQDAQASSRNSKKIPLEKRELKLARLRQLMQRSLSESDTDSNNSEDPKTTPVRKADRPRPQPIVESVESMDSAESLHLMIKKHTLASGGRRFPFSIKASKSLDGHSPSPTSESSEPDLESQYPGSGSIPPNQPSGDPQQPSPDSTAAQKVATSPKSALKSPSSKRRTSQNLKLRVTFEEPVVQMEQPSLELNGEKDKDKGRTLQRTSTSNESGDQLKRPFGAFRSIMETLSGNQNNNNNYQAANQLKTSTLPLTSLGRKTDAKGNPASSASKGKNKAA q8ney8-6 Periphilin-1 PPHLN1 Gastric cancer antigen Ga50 HSPC206 HSPC232 CDC7 expression repressor CR-S protein protein human Homo sapiens Human MAYRRDEMWSEGRYEYERIPRERAPPRSHPSDESGYRWTRDDHSASRQPEYRDMRDGFRRKSFYSSHYARERSPYKRDNTFFRESPVGRKDSPHSRSGSSVSSRSYSPERSKSYSFHQSQHRKSVRPGASYKRQNEGNPERDKERPVQSLKTSRDTSPSSGSAVSSSKVLDKPSRLTEKELAEAASKWAAEKLEKSDESNLPEISEYEAGSTAPLFTDQPEEPESNTTHGIELFEDSQLTTRSKAIASKTKEIEQVYRQDCETFGMVVKMLIEKDPSLEKSIQFALRQNLHEIGERCVEELKHFIAEYDTSTQDFGEPF Ref.3 (AAF36126) sequence differs from that shown due to frameshift. Ref.3 (AAF36152) sequence differs from that shown due to frameshift. pphln_mouse Periphilin-1 Pphln1 protein protein mouse Mus musculus Mouse MWSEGRYDYDRLPRERVPPRSHPSDGYHRVVNVVPKRPPLLDKRPPLLDKRPPLLARPDEGGYSRYYSHVDCRVCDEGRSFSHDRRSGPSHSGDESGYRWLRDDHSTSRQPDYRDMRDGFRRKSFYSSHYSRDRSPHKRDAPFFRESPVGRKDSPHSRSGSSVSSRSYSPERSRTHSFHQSQHRKSSRVGASYKRQNEAIRGRGKERSIQSVKTSRDASPSSSSAVASSKALDKPSRLTEKELAEAESKWANETLEKSDESNLAEMNEFEAGSTAPLFIDQTEEPESNTVDGTELYEDSQLSNRSKAIASKTKEIEQVYRQDCETFGMVVKMLIEKDPSLEKSVQFALRQNLHEIGERCVEELKRFITEYDNSARDFGDPF pphln_human Periphilin-1 Gastric cancer antigen Ga50 HSPC206 HSPC232 PPHLN1 CDC7 expression repressor protein protein human Homo sapiens Human MWSEGRYEYERIPRERAPPRSHPSDGYNRLVNIVPKKPPLLDRPGEGSYNRYYSHVDYRDYDEGRSFSHDRRSGPPHRGDESGYRWTRDDHSASRQPEYRDMRDGFRRKSFYSSHYARERSPYKRDNTFFRESPVGRKDSPHSRSGSSVSSRSYSPERSKSYSFHQSQHRKSVRPGASYKRQNEGNPERDKERPVQSLKTSRDTSPSSGSAVSSSKVLDKPSRLTEKELAEAASKWAAEKLEKSDESNLPEISEYEAGSTAPLFTDQPEEPESNTTHGIELFEDSQLTTRSKAIASKTKEIEQVYRQDCETFGMVVKMLIEKDPSLEKSIQFALRQNLHEIESAGQTWQQVPPVRNTEMDHDGTPENEGEETAQSAPQPPQAPQPLQPRKKRVRRTTQLRRTTGAPDITWGMLKKTTQEAERILLRTQTPFTPENLFLAMLSVVHCNSRKDVKPENKQ sncaip-pphln1 1479315 n/a 1479320 unspecified role unspecified role bait bait regions sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false n/a 1479321 unspecified role unspecified role prey prey physical association physical association false false false no figure sncaip-pphln1-1 1479316 n/a 1479321 unspecified role unspecified role prey prey region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false n/a 1479320 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false figure 2 sncaip-pphln1-2 1479317 n/a 1479322 unspecified role unspecified role prey prey n/a 1479320 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false figure 3 sncaip-pphln1-3 1479318 n/a 1479323 unspecified role unspecified role neutral component neutral component n/a 1479320 unspecified role unspecified role 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 colocalization colocalization false false false figure 4 a-c pphln1-pphln1 1479319 n/a 1479323 unspecified role unspecified role bait bait c_terminus 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 c_terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false n/a 1479320 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 physical association physical association false false false Supp fig 1