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/ w_tzlich-2013-2 The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo. in vitro In vitro pull down pull down weight by staining molecular weight estimation by staining weight by staining Wätzlich D., Vetter I., Gotthardt K., Miertzschke M., Chen Y.X., Wittinghofer A., Ismail S. Data on the identity, synthesis and features of F-Rheb (fully C-terminally S-farnesylated, carboxymethylated Rheb) was taken from PMID:22002721 and PMID:20652921. alfred.wittinghofer@mpi-dortmund.mpg.de,shehab.ismail@mpi-dortmund.mpg.de EMBO Rep. (1469-221X) 2013 Only protein-protein interactions imex curation w_tzlich-2013-4 The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by staining molecular weight estimation by staining weight by staining Wätzlich D., Vetter I., Gotthardt K., Miertzschke M., Chen Y.X., Wittinghofer A., Ismail S. alfred.wittinghofer@mpi-dortmund.mpg.de,shehab.ismail@mpi-dortmund.mpg.de EMBO Rep. (1469-221X) 2013 Only protein-protein interactions imex curation w_tzlich-2013-3 The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo. in vitro In vitro fps fluorescence polarization spectroscopy Fluorescence anisotropy FPS FPS Fluorescence anisotropy fps tag fluorescence tag visualisation by fluorescence tag fluorescence Wätzlich D., Vetter I., Gotthardt K., Miertzschke M., Chen Y.X., Wittinghofer A., Ismail S. Data on the identity, synthesis and features of F-Rheb (fully C-terminally S-farnesylated, carboxymethylated Rheb) and the C-terminal Rheb peptide was taken from PMID:22002721 and PMID:20652921. alfred.wittinghofer@mpi-dortmund.mpg.de,shehab.ismail@mpi-dortmund.mpg.de EMBO Rep. (1469-221X) 2013 Only protein-protein interactions imex curation w_tzlich-2013-1 The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Wätzlich D., Vetter I., Gotthardt K., Miertzschke M., Chen Y.X., Wittinghofer A., Ismail S. alfred.wittinghofer@mpi-dortmund.mpg.de,shehab.ismail@mpi-dortmund.mpg.de EMBO Rep. (1469-221X) 2013 Only protein-protein interactions imex curation pde6d_human Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Protein p17 PDE6D PDED protein protein human Homo sapiens Human MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV rpgr_human X-linked retinitis pigmentosa GTPase regulator RPGR RP3 XLRP3 protein protein human Homo sapiens Human MREPEELMPDSGAVFTFGKSKFAENNPGKFWFKNDVPVHLSCGDEHSAVVTGNNKLYMFGSNNWGQLGLGSKSAISKPTCVKALKPEKVKLAACGRNHTLVSTEGGNVYATGGNNEGQLGLGDTEERNTFHVISFFTSEHKIKQLSAGSNTSAALTEDGRLFMWGDNSEGQIGLKNVSNVCVPQQVTIGKPVSWISCGYYHSAFVTTDGELYVFGEPENGKLGLPNQLLGNHRTPQLVSEIPEKVIQVACGGEHTVVLTENAVYTFGLGQFGQLGLGTFLFETSEPKVIENIRDQTISYISCGENHTALITDIGLMYTFGDGRHGKLGLGLENFTNHFIPTLCSNFLRFIVKLVACGGCHMVVFAAPHRGVAKEIEFDEINDTCLSVATFLPYSSLTSGNVLQRTLSARMRRRERERSPDSFSMRRTLPPIEGTLGLSACFLPNSVFPRCSERNLQESVLSEQDLMQPEEPDYLLDEMTKEAEIDNSSTVESLGETTDILNMTHIMSLNSNEKSLKLSPVQKQKKQQTIGELTQDTALTENDDSDEYEEMSEMKEGKACKQHVSQGIFMTQPATTIEAFSDEEVGNDTGQVGPQADTDGEGLQKEVYRHENNNGVDQLDAKEIEKESDGGHSQKESEAEEIDSEKETKLAEIAGMKDLREREKSTKKMSPFFGNLPDRGMNTESEENKDFVKKRESCKQDVIFDSERESVEKPDSYMEGASESQQGIADGFQQPEAIEFSSGEKEDDEVETDQNIRYGRKLIEQGNEKETKPIISKSMAKYDFKCDRLSEIPEEKEGAEDSKGNGIEEQEVEANEENVKVHGGRKEKTEILSDDLTDKAEDHEFSKTEELKLEDVDEEINAENVESKKKTVGDDESVPTGYHSKTEGAERTNDDSSAETIEKKEKANLEERAICEYNENPKGYMLDDADSSSLEILENSETTPSKDMKKTKKIFLFKRVPSINQKIVKNNNEPLPEIKSIGDQIILKSDNKDADQNHMSQNHQNIPPTNTERRSKSCTIL q15382-pro_0000082708 GTP-binding protein Rheb RHEB RHEB2 Ras homolog enriched in brain protein protein human Homo sapiens Human MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKMDGAASQGKSSC 1 181 arl3_mouse ADP-ribosylation factor-like protein 3 Arl3 protein protein mouse Mus musculus Mouse MGLLSILRKLKSAPDQEVRILLLGLDNAGKTTLLKQLASEDISHITPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTAAPASEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNVNAKKK arl2_mouse ADP-ribosylation factor-like protein 2 Arl2 protein protein mouse Mus musculus Mouse MGLLTILKKMKQKERELRLLMLGLDNAGKTTILKKFNGEDVDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSCNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDISSRVFTAD pde6d-rpgr-5 1420372 n/a 1420376 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false O43924:p.Arg48Glu mutation disrupting mutation disrupting interaction mutation disrupting substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q92834:p.Glu216Arg mutation disrupting mutation disrupting interaction mutation disrupting substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction false false false Fig. 2f, Fig. 3b, Suppl. Fig. 3b, Suppl. Fig. 4 pde6d-rheb 1420372 n/a F-RheB 1420378 unspecified role unspecified role prey prey cys-181 sfarnomecys S-farnesyl-L-cysteine methyl ester SFarnOMeCys certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420376 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction false false false Fig 3b pde6d-rheb-1 1420372 n/a 1420376 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a F-RheB 1420378 unspecified role unspecified role prey prey cys181 sfarnomecys S-farnesyl-L-cysteine methyl ester SFarnOMeCys certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Fig. 3b arl3-pde6d-2 1420372 n/a 1420376 unspecified role unspecified role prey prey O43924:p.[Phe94Ala;Ile98Ala] mutation mutation substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420379 unspecified role unspecified role bait bait c-terminal 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 ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Suppl. Fig. 6c The authors claim that a ternary Pde6d-RPGR-Arl3 complex could not be identified in pull down experiments using His-tagged Arl3 as bait with RPGR and wild type Pde6d as prey. pde6d-arl2 1420372 n/a 1420376 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420380 competitor competitor competitor prey prey ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Suppl. Fig. 6a Arl2 is bound to non-hydrolysable GTP analogue GppNHp. pde6d-arl3 1420372 n/a 1420379 competitor competitor competitor prey prey ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420376 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Suppl. Fig. 6b Arl3 is bound to non-hydrolysable GTP analogue GppNHp. arl3-pde6d-1 1420373 n/a 1420377 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420376 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420379 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Fig. 3e pde6d-rpgr-7 1420373 n/a 1420377 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420376 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction false false false Fig. 3f arl2-pde6d-4 1420373 n/a 1420376 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420380 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction false false false Fig. 3f arl2-pde6d-5 1420373 n/a 1420380 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420376 unspecified role unspecified role neutral component neutral component O43924:p.[Phe94Ala;Ile98Ala] mutation mutation substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Fig. 3g The phe94ala-ile98ala Pde6d mutant forms a stable ternary complex with RPGR and Arl2, while for wild type Pde6d only the binary Pde6d-RPGR and Pde6d-Arl2 complexes were observed. arl3-pde6d-3 1420373 n/a 1420379 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420376 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction false false false Fig. 3e pde6d-rpgr-6 1420374 n/a 1420376 unspecified role unspecified role neutral component neutral component region cy5 label cy5 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction false false false 1420374 Fig. 3c, Suppl. Fig. 3a Temp = 20C; pH = 7.5 pde6d-rheb-2 1420374 n/a 1420376 unspecified role unspecified role neutral component neutral component region cy5 label cy5 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420377 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a F-RheB 1420378 unspecified role unspecified role neutral component neutral component cys181 sfarnomecys S-farnesyl-L-cysteine methyl ester SFarnOMeCys 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 ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Fig. 3c Temp = 20C; pH = 7.5 pde6d-rheb-3 1420374 n/a 1420378 unspecified role unspecified role neutral component neutral component cys174 fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false cys181 sfarnomecys S-farnesyl-L-cysteine methyl ester SFarnOMeCys certain certain sequence position certain certain certain sequence position certain false Q15382-PRO_0000082708:p.Ala174Cys 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 1420376 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) direct interaction direct interaction false false false 1420374 1420374 Fig. 4b, Suppl. Fig. 5 Temp = 20C; pH = 7.5 The presence of RPGR had no effect on the association or dissociation rate constants of the Rheb-Pde6d interaction. pde6d-rheb-4 1420374 n/a 1420377 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) n/a 1420378 unspecified role unspecified role neutral component neutral component cys181 sfarnomecys S-farnesyl-L-cysteine methyl ester SFarnOMeCys certain certain sequence position certain certain certain sequence position certain false cys174 fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false Q15382-PRO_0000082708:p.Ala174Cys 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 1420376 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) physical association physical association false false false Fig 4b Temp = 20C; pH = 7.5 Addition of non-hydrolysable GTP analogue GppNHp-bound Arl3 resulted in dissociation of the complex. pde6d-rpgr-4 1420375 n/a 1420376 unspecified role unspecified role neutral component neutral component ecobd Escherichia coli (strain B / BL21-DE3) Stoichiometry: 1.0 n/a 1420377 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobd Escherichia coli (strain B / BL21-DE3) Stoichiometry: 1.0 direct interaction direct interaction false false false Fig. 2c, Fig. 2d, Fig. 2f, Suppl. table 1 1.90A working 19.9%, free 22.1%