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/ iles-2007-1 APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. 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 Iles N., Rulten S., El-Khamisy SF., Caldecott KW. k.w.caldecott@sussex.ac.uk Mol. Cell. Biol. (0270-7306) 2007 Only protein-protein interactions imex curation iles-2007-2 APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Iles N., Rulten S., El-Khamisy SF., Caldecott KW. k.w.caldecott@sussex.ac.uk Mol. Cell. Biol. (0270-7306) 2007 Only protein-protein interactions imex curation iles-2007-3 APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. human-a_549 Homo sapiens Caucasian lung carcinoma cell line a_549 Human Caucasian lung carcinoma anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Iles N., Rulten S., El-Khamisy SF., Caldecott KW. k.w.caldecott@sussex.ac.uk Mol. Cell. Biol. (0270-7306) 2007 Only protein-protein interactions imex curation iles-2007-4 APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. in vitro In vitro filter binding filter binding Filter overlay assay Filter overlay assay antibody detection identification by antibody antibody detection Iles N., Rulten S., El-Khamisy SF., Caldecott KW. k.w.caldecott@sussex.ac.uk Mol. Cell. Biol. (0270-7306) 2007 Only protein-protein interactions imex curation iles-2007-5 APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. in vitro In vitro far western blotting far western blotting Affinity blotting Affinity blotting western blot western blot Immuno blot Immuno blot Iles N., Rulten S., El-Khamisy SF., Caldecott KW. k.w.caldecott@sussex.ac.uk Mol. Cell. Biol. (0270-7306) 2007 Only protein-protein interactions imex curation iles-2007-6 APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. human-a_549 Homo sapiens Caucasian lung carcinoma cell line a_549 Human Caucasian lung carcinoma fluorescence imaging fluorescence microscopy fluorescence imaging immunostaining immunostaining Iles N., Rulten S., El-Khamisy SF., Caldecott KW. k.w.caldecott@sussex.ac.uk Mol. Cell. Biol. (0270-7306) 2007 Only protein-protein interactions imex curation iles-2007-7 APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. fluorescence imaging fluorescence microscopy fluorescence imaging immunostaining immunostaining Iles N., Rulten S., El-Khamisy SF., Caldecott KW. k.w.caldecott@sussex.ac.uk Mol. Cell. Biol. (0270-7306) 2007 Only protein-protein interactions imex curation xrcc1_human DNA repair protein XRCC1 XRCC1 X-ray repair cross-complementing protein 1 protein protein human Homo sapiens Human MPEIRLRHVVSCSSQDSTHCAENLLKADTYRKWRAAKAGEKTISVVLQLEKEEQIHSVDIGNDGSAFVEVLVGSSAGGAGEQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGPDKLVRAAAEKRWDRVKIVCSQPYSKDSPFGLSFVRFHSPPDKDEAEAPSQKVTVTKLGQFRVKEEDESANSLRPGALFFSRINKTSPVTASDPAGPSYAAATLQASSAASSASPVSRAIGSTSKPQESPKGKRKLDLNQEEKKTPSKPPAQLSPSVPKRPKLPAPTRTPATAPVPARAQGAVTGKPRGEGTEPRRPRAGPEELGKILQGVVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLGLGGRIVRKEWVLDCHRMRRRLPSRRYLMAGPGSSSEEDEASHSGGSGDEAPKLPQKQPQTKTKPTQAAGPSSPQKPPTPEETKAASPVLQEDIDIEGVQSEGQDNGAEDSGDTEDELRRVAEQKEHRLPPGQEENGEDPYAGSTDENTDSEEHQEPPDLPVPELPDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDNMSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNEKQKLLPHQLYGVVPQA aplf_human Aprataxin and PNK-like factor APLF C2orf13 PALF XIP1 Apurinic-apyrimidinic endonuclease APLF PNK and APTX-like FHA domain-containing protein XRCC1-interacting protein 1 protein protein human Homo sapiens Human MSGGFELQPRDGGPRVALAPGETVIGRGPLLGITDKRVSRRHAILEVAGGQLRIKPIHTNPCFYQSSEKSQLLPLKPNLWCYLNPGDSFSLLVDKYIFRILSIPSEVEMQCTLRNSQVLDEDNILNETPKSPVINLPHETTGASQLEGSTEIAKTQMTPTNSVSFLGENRDCNKQQPILAERKRILPTWMLAEHLSDQNLSVPAISGGNVIQGSGKEEICKDKSQLNTTQQGRRQLISSGSSENTSAEQDTGEECKNTDQEESTISSKEMPQSFSAITLSNTEMNNIKTNAQRNKLPIEELGKVSKHKIATKRTPHKEDEAMSCSENCSSAQGDSLQDESQGSHSESSSNPSNPETLHAKATDSVLQGSEGNKVKRTSCMYGANCYRKNPVHFQHFSHPGDSDYGGVQIVGQDETDDRPECPYGPSCYRKNPQHKIEYRHNTLPVRNVLDEDNDNVGQPNEYDLNDSFLDDEEEDYEPTDEDSDWEPGKEDEEKEDVEELLKEAKRFMKRK xrcc4_human DNA repair protein XRCC4 X-ray repair cross-complementing protein 4 XRCC4 protein protein human Homo sapiens Human MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSRPDSSLPETSKKEHISAENMSLETLRNSSPEDLFDEI apfl-xrcc1-1 Interaction between APFL and XRCC1 identifed by Y2H 609566 N/A 609573 unspecified role unspecified role prey prey N/A 609574 unspecified role unspecified role bait bait physical association physical association false false false 2A apfl-xrcc4-1 Interaction between APFL and XRCC4 identifed by Y2H 609566 N/A 609575 unspecified role unspecified role prey prey N/A 609574 unspecified role unspecified role bait bait physical association physical association false false false 2A apfl-xrcc1-2 Interaction between APFL and XRCC1 identifed by coimmunoprecipitation 609567 N/A 609573 unspecified role unspecified role prey prey N/A 609574 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 2B apfl-xrcc1-3 Interaction between APFL and XRCC1 identifed by coimmunoprecipitation 609568 N/A 609574 unspecified role unspecified role prey prey N/A 609573 unspecified role unspecified role bait bait ser-485 (possible) opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false thr-488 (possible) opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 2C apfl-xrcc1-4 Interaction between APFL and XRCC1 identifed by filter binding 609569 N/A 609573 unspecified role unspecified role prey prey ser-485 (possible) opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false thr-488 (possible) opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false ser-518 (possible) opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false thr-519 (possible) opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false thr-523 (possible) opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false 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 ecoli Escherichia coli (strain K12) N/A 609574 unspecified role unspecified role bait bait fha region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false 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 ecoli Escherichia coli (strain K12) physical association physical association false false false 3B. 3C Ser-519 and Ser-523 described in the paper, actually appear to be threonine residues. APLF interacts with the phosphorylated form of XRCC1. The phosphorylated residues were first identified by incubating the XRCC1 with CK2 under the same conditions as used in this experiment and demonstrating site specific phosphorylation by use of the appropriate antibodies. apfl-xrcc1-5 Interaction between APFL and XRCC1 identifed by Far Western 609570 N/A 609574 unspecified role unspecified role prey prey fha region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false 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 ecoli Escherichia coli (strain K12) N/A 609573 unspecified role unspecified role bait bait ser-485 (possible) opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false thr-488 (possible) opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false ser-518 (possible) opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false thr-519 (possible) opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false thr-523 (possible) opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false 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 ecoli Escherichia coli (strain K12) physical association physical association false false false 3D Ser-519 and Ser-523 described in the paper, actually appear to be threonine residues. APLF interacts with the phosphorylated form of XRCC1. The phosphorylated residues were first identified by incubating the XRCC1 with CK2 under the same conditions as used in this experiment and demonstrating site specific phosphorylation by use of the appropriate antibodies. apfl-xrcc1-6 Interaction between APFL and XRCC1 identifed by colocalisation 609571 N/A 609573 unspecified role unspecified role neutral component neutral component N/A 609574 unspecified role unspecified role neutral component neutral component physical association physical association false false false 4A 0.35 uJ/um2 UVA apfl-xrcc1-7 Interaction between APFL and XRCC1 identifed by colocalisation 609572 N/A 609574 unspecified role unspecified role neutral component neutral component region yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Q8IW19:p.Arg27Ala mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false N/A 609573 unspecified role unspecified role neutral component neutral component region rfp tag red fluorescent protein tag red fluorescent protein RFP red fluorescent protein RFP rfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false 4C 10 mM H2O2 for 10 min Arg27Ala mutant of APLF remains in the cytoplasm after hydrogen peroxide treatment.