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/ gijsbers-2018-1 in vitro In vitro fps fluorescence polarization spectroscopy Fluorescence anisotropy FPS FPS Fluorescence anisotropy fps predetermined predetermined participant predetermined Gijsbers A., Montagut DC., Méndez-Godoy A., Altamura D., Saviano M., Siliqi D., Sánchez-Puig N. dritan.siliqi@ic.cnr.it,nuriasp@unam.mx International journal of molecular sciences 2018 Only protein-protein interactions imex curation imex curation gijsbers-2018-2 in vitro In vitro saxs x ray scattering saxs predetermined predetermined participant predetermined Gijsbers A., Montagut DC., Méndez-Godoy A., Altamura D., Saviano M., Siliqi D., Sánchez-Puig N. dritan.siliqi@ic.cnr.it,nuriasp@unam.mx International journal of molecular sciences 2018 Only protein-protein interactions imex curation imex curation gijsbers-2018-3 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 Gijsbers A., Montagut DC., Méndez-Godoy A., Altamura D., Saviano M., Siliqi D., Sánchez-Puig N. dritan.siliqi@ic.cnr.it,nuriasp@unam.mx International journal of molecular sciences 2018 Only protein-protein interactions imex curation imex curation efl1_human Elongation factor-like GTPase 1 EFL1 EFTUD1 Elongation factor Tu GTP-binding domain-containing protein 1 Elongation factor-like 1 FAM42A Protein FAM42A protein protein human Homo sapiens Human MVLNSLDKMIQLQKNTANIRNICVLAHVDHGKTTLADCLISSNGIISSRLAGKLRYMDSREDEQIRGITMKSSAISLHYATGNEEYLINLIDSPGHVDFSSEVSTAVRICDGCIIVVDAVEGVCPQTQAVLRQAWLENIRPVLVINKIDRLIVELKFTPQEAYSHLKNILEQINALTGTLFTSKVLEERAERETESQVNPNSEQGEQVYDWSTGLEDTDDSHLYFSPEQGNVVFTSAIDGWGFGIEHFARIYSQKIGIKKEVLMKTLWGDYYINMKAKKIMKGDQAKGKKPLFVQLILENIWSLYDAVLKKDKDKIDKIVTSLGLKIGAREARHSDPKVQINAICSQWLPISHAVLAMVCQKLPSPLDITAERVERLMCTGSQTFDSFPPETQALKAAFMKCGSEDTAPVIIFVSKMFAVDAKALPQNKPRPLTQEEIAQRRERARQRHAEKLAAAQGQAPLEPTQDGSAIETCPKGEEPRGDEQQVESMTPKPVLQEENNQESFIAFARVFSGVARRGKKIFVLGPKYSPLEFLRRVPLGFSAPPDGLPQVPHMAYCALENLYLLMGRELEYLEEVPPGNVLGIGGLQDFVLKSATLCSLPSCPPFIPLNFEATPIVRVAVEPKHPSEMPQLVKGMKLLNQADPCVQILIQETGEHVLVTAGEVHLQRCLDDLKERFAKIHISVSEPIIPFRETITKPPKVDMVNEEIGKQQKVAVIHQMKEDQSKIPEGIQVDSDGLITITTPNKLATLSVRAMPLPEEVTQILEENSDLIRSMEQLTSSLNEGENTHMIHQKTQEKIWEFKGKLEQHLTGRRWRNIVDQIWSFGPRKCGPNILVNKSEDFQNSVWTGPADKASKEASRYRDLGNSIVSGFQLATLSGPMCEEPLMGVCFVLEKWDLSKFEEQGASDLAKEGQEENETCSGGNENQELQDGCSEAFEKRTSQKGESPLTDCYGPFSGQLIATMKEACRYALQVKPQRLMAAMYTCDIMATGDVLGRVYAVLSKREGRVLQEEMKEGTDMFIIKAVLPVAESFGFADEIRKRTSGLASPQLVFSHWEIIPSDPFWVPTTEEEYLHFGEKADSENQARKYMNAVRKRKGLYVEEKIVEHAEKQRTLSKNK sbds_human Ribosome maturation protein SBDS Shwachman-Bodian-Diamond syndrome protein SBDS CGI-97 protein protein human Homo sapiens Human MSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE ria1_yeast Ribosome assembly protein 1 YNL163C N1718 EFL1 Elongation factor-like 1 EF-2-like GTPase RIA1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MPRVESETYKRLQNDPSCIRNICIVAHVDHGKTSLSDSLLASNGIISQRLAGKIRFLDARPDEQLRGITMESSAISLYFRVLRKQEGSDEPLVSEHLVNLIDSPGHIDFSSEVSAASRLCDGAVVLVDVVEGVCSQTVTVLRQCWTEKLKPILVLNKIDRLITELQLTPQEAYIHLSKVIEQVNSVIGSFFANERQLDDLFWREQLEKNENAEYIEKDDSGIYFNPTDNNVIFASAIDGWGFNIGQLAKFYEQKLGAKRENLQKVLWGDFYMDPKTKKIINNKGLKGRSLKPLFTSLILENIWKIYQNIITSRDSEMVEKIAKTLNIKLLARDLRSKDDKQLLRTIMGQWLPVSTAVLLTVIEKLPSPLESQTDRLNTILVSESDTAAMDPRLLKAMKTCDKEGPVSAYVSKMLSIPREELPVESKRIASSDELMERSRKAREEALNAAKHAGMVENMAMMDLNDNSKNTSDLYKRAKDTVMTPEVGEQTKPKPSRNNDVFCVVSEPSSALDLEFEYEGEDDSDSQDNFGLDFVPTDIDPNDPLSSMFEYEEEDPLLESIKQISEDVNDEVDDIFDEKEECLVAFARIYSGTLRVGQEISVLGPKYDPKCPEEHIETAIITHLYLFMGKELVPLDVCPSGNIVGIRGLAGKVLKSGTLIEKGVQGVNLAGVNFHFTPIVRVAVEPANPVEMSKLVRGLKLLDQADPCVHTYVENTGEHILCTAGELHLERCLKDLTERFAGIEITHSEPAIPYRETFLSASDMNPPQNSQLGRGVHELLLSQYKITFRTFPLSGKVTDFLSQHQNSIKNILKTSTSSMDPVIESTGSSFLDKKSLLVAFEEVINQEEKSRELLSGFKVKLAGFGPSRVGCNILLSQDNLLGSLFEGTPAAFEYSDSIKNGFQLAVSEGPLANEPVQGMCVLVESVHKMSQDEIESIEDPRYQQHIVDLSGRLITSTRDAIHEAFLDWSPRIMWAIYSCDIQTSVDVLGKVYAVILQRHGKIISEEMKEGTPFFQIEAHVPVVEAFGLSEDIRKRTSGAAQPQLVFSGFECIDLDPFWVPTTEEELEELGDTADRENIARKHMNAIRRRKGLFIEEKVVENAEKQRTLKKN sdo1_yeast Ribosome maturation protein SDO1 YLR022C SDO1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MPINQPSGQIKLTNVSLVRLKKARKRFEVACYQNKVQDYRKGIEKDLDEVLQIHQVFMNVSKGLVANKEDLQKCFGTTNVDDVIEEIMHKGEIQLSEKERQLMLNKVNNEMLTIVSAKCINPVSKKRYPPTMIHKALQELKFSPVINKPAKLQALEAIKLLVSKQIIPIVRAKMKVKVAISEPSRQPELIEKISKLIASSPGESTKPELDPWTCTGLIDPVNYRDLMTLCDKKGTVQVLDMAVIDNTTHN efl1-sbds-1 3580955 N/A 3580958 unspecified role unspecified role neutral component neutral component purified purified 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 yeast Saccharomyces cerevisiae Baker's yeast N/A 3580959 unspecified role unspecified role neutral component neutral component purified purified Q9Y3A5:p.Arg19Gln mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Kd1 (µM) = 4.2; Kd2 (µM) = 5.2 Q9Y3A5:p.Lys67Glu mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Kd1 (µM) = 7.2; Kd2 (µM) = 3 C-terminus fiash label fiash label FIAsH label 4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein FIAsH label c-term range C-terminal range c-term range c-term range C-terminal range c-term range false Q9Y3A5:p.Arg126Thr mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Kd1 (µM) = 9.3; Kd2 (µM) = 2.5 Q9Y3A5:p.Ser143Leu mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false Q9Y3A5:p.Ile167Thr mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Kd1 (µM) = 10; Kd2 (µM) = 1.4 Q9Y3A5:p.Arg175Trp mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Kd1 (µM) = 12; Kd2 (µM) = 3.3 Q9Y3A5:p.Ile212Thr mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false domain 2-3 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false domain 1-2 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false Kd1 (µM) - 11.3; Kd2 (µM) - 3.9 domain 1 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false domain 2 binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false region xpress tag xpress tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3580955 3580955 Table 1, Figure 1, 2 A two distinct binding sites model with positive cooperativity best describes the interaction [Kd1-Domain 1 (residues 1-94); Kd2 - Domain 2 (residues 94-175): Kd1 (µM) = 5.4; Kd2 (µM) = 0.4]; Hill coefficient -1.8. Mutations were tested on full length construct. ria1-sdo1-1 3580956 N/A 3580960 unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 N/A 3580961 unspecified role unspecified role neutral component neutral component purified purified yeast Saccharomyces cerevisiae Baker's yeast Stoichiometry: 1.0 direct interaction direct interaction false false false Figures 3, 4; Supplementary tables 1, 2 Small Angle Biological Data Bank accession code: SASDET8 Resolution (Å) - 38 ria1-sdo1-2 3580957 N/A 3580960 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed n-terminal region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3580961 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell domains 2+3 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 Supplemental figure 2