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/ naidu-2013-1 in vitro In vitro elisa enzyme linked immunosorbent assay ELISA ELISA elisa antibody detection identification by antibody antibody detection Naidu VG., Dinesh Babu KR., Thwin MM., Satish RL., Kumar PV., Gopalakrishnakone P. ELISA results are stated to be given in Table 1- however they appear to be in Table 2. Human sRANKL (PromoKine) is stated to be a single, non-glycosylated polypeptide chain of 176 amino acids; however no sequence/amino acid range is stated. Thus an identifier was taken from UniProt O14788-PRO_0000034515 (-amino acids 140-317). antgopal@nus.edu.sg Chemico-biological interactions 2013 imex curation Only protein-protein interactions imex curation naidu-2013-2 in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Naidu VG., Dinesh Babu KR., Thwin MM., Satish RL., Kumar PV., Gopalakrishnakone P. Human sRANKL (PromoKine) is stated to be a single, non-glycosylated polypeptide chain of 176 amino acids; however no sequence/amino acid range is stated. Thus an identifier was taken from UniProt O14788-PRO_0000034515 (-amino acids 140-317). antgopal@nus.edu.sg Chemico-biological interactions 2013 imex curation Only protein-protein interactions imex curation o14788-pro_0000034515 Tumor necrosis factor ligand superfamily member 11, soluble form TNFSF11 OPGL RANKL TRANCE Osteoclast differentiation factor Osteoprotegerin ligand Receptor activator of nuclear factor kappa-B ligand TNF-related activation-induced cytokine protein protein human Homo sapiens Human IRAEKAMVDGSWLDLAKRSKLEAQPFAHLTINATDIPSGSHKVSLSSWYHDRGWAKISNMTFSNGKLIVNQDGFYYLYANICFRHHETSGDLATEYLQLMVYVTKTSIKIPSSHTLMKGGSTKYWSGNSEFHFYSINVGGFFKLRSGEEISIEVSNPSLLDPDQDATYFGAFKVRDID 140 317 tnr11_human Tumor necrosis factor receptor superfamily member 11A Receptor activator of NF-KB Osteoclast differentiation factor receptor TNFRSF11A RANK protein protein human Homo sapiens Human MAPRARRRRPLFALLLLCALLARLQVALQIAPPCTSEKHYEHLGRCCNKCEPGKYMSSKCTTTSDSVCLPCGPDEYLDSWNEEDKCLLHKVCDTGKALVAVVAGNSTTPRRCACTAGYHWSQDCECCRRNTECAPGLGAQHPLQLNKDTVCKPCLAGYFSDAFSSTDKCRPWTNCTFLGKRVEHHGTEKSDAVCSSSLPARKPPNEPHVYLPGLIILLLFASVALVAAIIFGVCYRKKGKALTANLWHWINEACGRLSGDKESSGDSCVSTHTANFGQQGACEGVLLLTLEEKTFPEDMCYPDQGGVCQGTCVGGGPYAQGEDARMLSLVSKTEIEEDSFRQMPTEDEYMDRPSQPTDQLLFLTEPGSKSTPPFSEPLEVGENDSLSQCFTGTQSTVGSESCNCTEPLCRTDWTPMSSENYLQKEVDSGHCPHWAASPSPNWADVCTGCRNPPGEDCEPLVGSPKRGPLPQCAYGMGLPPEEEASRTEARDQPEDGADGRLPSSARAGAGSGSSPGGQSPASGNVTGNSNSTFISSGQVMNFKGDIIVVYVSQTSQEGAAAAAEPMGRPVQEETLARRDSFAGNGPRFPDPCGGPEGLREPEKASRPVQEQGGAKA tr11b_human Tumor necrosis factor receptor superfamily member 11B OCIF OPG TNFRSF11B Osteoclastogenesis inhibitory factor Osteoprotegerin protein protein human Homo sapiens Human MNNLLCCALVFLDISIKWTTQETFPPKYLHYDEETSHQLLCDKCPPGTYLKQHCTAKWKTVCAPCPDHYYTDSWHTSDECLYCSPVCKELQYVKQECNRTHNRVCECKEGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNATHDNICSGNSESTQKCGIDVTLCEEAFFRFAVPTKFTPNWLSVLVDNLPGTKVNAESVERIKRQHSSQEQTFQLLKLWKHQNKDQDIVKKIIQDIDLCENSVQRHIGHANLTFEQLRSLMESLPGKKVGAEDIEKTIKACKPSDQILKLLSLWRIKNGDQDTLKGLMHALKHSKTYHFPKTVTQSLKKTIRFLHSFTMYKLYQKLFLEMIGNQVQSVKISCL tnfrsf11a-tnfsf11-2 2972439 N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Table 2 (1) tnfrsf11a-tnfsf11-3 2972439 N/A 2972443 inhibitor inhibitor unspecified role unspecified role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Table 2 (1) i Peptide (10uM) inhibition on RANKL binding to the RANK receptor = 65% tnfrsf11a-tnfsf11-4 2972439 N/A 2972443 inhibitor inhibitor unspecified role unspecified role cys118 xlnk-scys-scys L-cystine (cross-link) (2R,2'R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid) 3,3'-disulfane-1,2-diylbis(2-azanylpropanoic acid) 3,3'-dithiobis(2-aminopropanoic acid) 3,3'-dithiobisalanine 3,3'-dithiodialanine beta,beta'-diamino-beta,beta'-dicarboxydiethyldisulfide beta,beta'-dithiodialanine DISULFID DISULFID Interchain L-cystine bis(alpha-aminopropionic acid)-beta-disulfide bis(beta-amino-beta-carboxyethyl)disulfide dicysteine 2-amino-3-(2-amino-2-carboxy-ethyl)disulfanyl-propanoic acid Cys2 Cystine ((Cys)2) XLNK-SCys-SCys certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false O00300:p.His121Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 2972456 2972458 physical association physical association false false false Table 2 (1) ii Peptide (10uM) inhibition on RANKL binding to the RANK receptor = 8% tnfrsf11a-tnfsf11-5 2972439 N/A 2972443 inhibitor inhibitor unspecified role unspecified role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false O00300:p.Cys118Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Table 2 (1) iii Peptide (10uM) inhibition on RANKL binding to the RANK receptor = 93% tnfrsf11a-tnfsf11-6 2972439 N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 2972443 inhibitor inhibitor unspecified role unspecified role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) physical association physical association false false false Table 2 (1) iv Peptide (10uM) inhibition on RANKL binding to the RANK receptor = 20% tnfrsf11a-tnfsf11-7 2972439 N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 2972443 inhibitor inhibitor unspecified role unspecified role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) physical association physical association false false false Table 2 (1) v Peptide (10uM) inhibition on RANKL binding to the RANK receptor = 12% tnfrsf11a-tnfsf11-8 2972439 N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 2972443 inhibitor inhibitor unspecified role unspecified role region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) physical association physical association false false false Table 2 (1) vi Peptide (10uM) inhibition on RANKL binding to the RANK receptor = 10% tnfrsf11a-tnfsf11-9 2972440 N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 1 tnfrsf11a-tnfsf11-10 2972440 N/A 2972443 inhibitor inhibitor unspecified role unspecified role O00300:p.Cys118Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 2972441 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) N/A 2972442 unspecified role unspecified role bait bait partial_ecd sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig 1i