DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases. Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Chen X., Liu H., Focia P.J., Shim A.H., He X. Cardiac - Interactions involving cardiac related proteins Contradiction wrt His-tag between methods and PDBe. S1 methods states: Purified M-CSF and FMS proteins were digested with bovine carboxypeptidase A (Sigma) to cleave off the His-tag. Whereas PDBe entry includes the His-tag in primary structure Supporting data doc: mouse M-CSF receptor-binding domain (residues 4-50 of the mature peptide). UniProt list mature protein as starting at residue 33 extracellular domains of mouse FMS (residues 20-299 for domains 1-3 and residues 20-511 for domains 1-5) x-he@northwestern.edu 09-Sep-2013: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Chen X., Liu H., Focia P.J., Shim A.H., He X. Cardiac - Interactions involving cardiac related proteins Contradiction wrt His-tag between methods and PDBe. S1 methods states: Purified M-CSF and FMS proteins were digested with bovine carboxypeptidase A (Sigma) to cleave off the His-tag. Whereas PDBe entry includes the His-tag in primary structure Supporting data doc: mouse M-CSF receptor-binding domain (residues 4-50 of the mature peptide). UniProt list mature protein as starting at residue 33 extracellular domains of mouse FMS (residues 20-299 for domains 1-3 and residues 20-511 for domains 1-5) x-he@northwestern.edu Accepted 2013-AUG-13 by ORCHARD 09-Sep-2013: Contacted by IntAct-Help. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases. Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Chen X., Liu H., Focia P.J., Shim A.H., He X. Cardiac - Interactions involving cardiac related proteins Contradiction wrt His-tag between methods and PDBe. S1 methods states: Purified M-CSF and FMS proteins were digested with bovine carboxypeptidase A (Sigma) to cleave off the His-tag. Whereas PDBe entry includes the His-tag in primary structure Supporting data doc: mouse M-CSF receptor-binding domain (residues 4-50 of the mature peptide). UniProt list mature protein as starting at residue 33 extracellular domains of mouse FMS (residues 20-299 for domains 1-3 and residues 20-511 for domains 1-5) x-he@northwestern.edu 09-Sep-2013: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Chen X., Liu H., Focia P.J., Shim A.H., He X. Cardiac - Interactions involving cardiac related proteins Contradiction wrt His-tag between methods and PDBe. S1 methods states: Purified M-CSF and FMS proteins were digested with bovine carboxypeptidase A (Sigma) to cleave off the His-tag. Whereas PDBe entry includes the His-tag in primary structure Supporting data doc: mouse M-CSF receptor-binding domain (residues 4-50 of the mature peptide). UniProt list mature protein as starting at residue 33 extracellular domains of mouse FMS (residues 20-299 for domains 1-3 and residues 20-511 for domains 1-5) x-he@northwestern.edu Accepted 2013-AUG-13 by ORCHARD 09-Sep-2013: Contacted by IntAct-Help. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases. Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Chen X., Liu H., Focia P.J., Shim A.H., He X. Cardiac - Interactions involving cardiac related proteins Contradiction wrt His-tag between methods and PDBe. S1 methods states: Purified M-CSF and FMS proteins were digested with bovine carboxypeptidase A (Sigma) to cleave off the His-tag. Whereas PDBe entry includes the His-tag in primary structure Supporting data doc: mouse M-CSF receptor-binding domain (residues 4-50 of the mature peptide). UniProt list mature protein as starting at residue 33 extracellular domains of mouse FMS (residues 20-299 for domains 1-3 and residues 20-511 for domains 1-5) x-he@northwestern.edu 09-Sep-2013: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Chen X., Liu H., Focia P.J., Shim A.H., He X. Cardiac - Interactions involving cardiac related proteins Contradiction wrt His-tag between methods and PDBe. S1 methods states: Purified M-CSF and FMS proteins were digested with bovine carboxypeptidase A (Sigma) to cleave off the His-tag. Whereas PDBe entry includes the His-tag in primary structure Supporting data doc: mouse M-CSF receptor-binding domain (residues 4-50 of the mature peptide). UniProt list mature protein as starting at residue 33 extracellular domains of mouse FMS (residues 20-299 for domains 1-3 and residues 20-511 for domains 1-5) x-he@northwestern.edu Accepted 2013-AUG-13 by ORCHARD 09-Sep-2013: Contacted by IntAct-Help. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation csf1_mouse Macrophage colony-stimulating factor 1 Csf1 Csfm protein protein mouse Mus musculus Mouse MTARGAAGRCPSSTWLGSRLLLVCLLMSRSIAKEVSEHCSHMIGNGHLKVLQQLIDSQMETSCQIAFEFVDQEQLDDPVCYLKKAFFLVQDIIDETMRFKDNTPNANATERLQELSNNLNSCFTKDYEEQNKACVRTFHETPLQLLEKIKNFFNETKNLLEKDWNIFTKNCNNSFAKCSSRDVVTKPDCNCLYPKATPSSDPASASPHQPPAPSMAPLAGLAWDDSQRTEGSSLLPSELPLRIEDPGSAKQRPPRSTCQTLESTEQPNHGDRLTEDSQPHPSAGGPVPGVEDILESSLGTNWVLEEASGEASEGFLTQEAKFSPSTPVGGSIQAETDRPRALSASPFPKSTEDQKPVDITDRPLTEVNPMRPIGQTQNNTPEKTDGTSTLREDHQEPGSPHIATPNPQRVSNSATPVAQLLLPKSHSWGIVLPLGELEGKRSTRDRRSPAELEGGSASEGAARPVARFNSIPLTDTGHVEQHEGSSDPQIPESVFHLLVPGIILVLLTVGGLLFYKWKWRSHRDPQTLDSSVGRPEDSSLTQDEDRQVELPV DIP protein P07141 original sequence version: 88 DIP protein P07141-1 original sequence version: 117 DIP protein P07141 original sequence version: 122 3886D72D70E770AF csf1r_mouse Macrophage colony-stimulating factor 1 receptor Csf1r Csfmr Fms CSF-1 receptor Proto-oncogene c-Fms protein protein mouse Mus musculus Mouse MELGPPLVLLLATVWHGQGAPVIEPSGPELVVEPGETVTLRCVSNGSVEWDGPISPYWTLDPESPGSTLTTRNATFKNTGTYRCTELEDPMAGSTTIHLYVKDPAHSWNLLAQEVTVVEGQEAVLPCLITDPALKDSVSLMREGGRQVLRKTVYFFSPWRGFIIRKAKVLDSNTYVCKTMVNGRESTSTGIWLKVNRVHPEPPQIKLEPSKLVRIRGEAAQIVCSATNAEVGFNVILKRGDTKLEIPLNSDFQDNYYKKVRALSLNAVDFQDAGIYSCVASNDVGTRTATMNFQVVESAYLNLTSEQSLLQEVSVGDSLILTVHADAYPSIQHYNWTYLGPFFEDQRKLEFITQRAIYRYTFKLFLNRVKASEAGQYFLMAQNKAGWNNLTFELTLRYPPEVSVTWMPVNGSDVLFCDVSGYPQPSVTWMECRGHTDRCDEAQALQVWNDTHPEVLSQKPFDKVIIQSQLPIGTLKHNMTYFCKTHNSVGNSSQYFRAVSLGQSKQLPDESLFTPVVVACMSVMSLLVLLLLLLLYKYKQKPKYQVRWKIIERYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLVITEYCCYGDLLNFLRRKAEAMLGPSLSPGQDSEGDSSYKNIHLEKKYVRRDSGFSSQGVDTYVEMRPVSTSSSDSFFKQDLDKEASRPLELWDLLHFSSQVAQGMAFLASKNCIHRDVAARNVLLTSGHVAKIGDFGLARDIMNDSNYVVKGNARLPVKWMAPESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNNKFYKLVKDGYQMAQPVFAPKNIYSIMQSCWDLEPTRRPTFQQICFLLQEQARLERRDQDYANLPSSGGSSGSDSGGGSSGGSSSEPEEESSSEHLACCEPGDIAQPLLQPNNYQFC DIP protein P09581 original sequence version: 115 DIP protein P09581 original sequence version: 149 DIP protein P09581 original sequence version: 160 DIP protein P09581 original sequence version: 156 7EDF8310CCF98906 csf1-csf1r-6 1 5 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 trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 4 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 trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. Resolution: 2.4 Å R-factor: 24.1%, Free R-factor: 26.5% 10 8 direct interaction direct interaction Table S1 R-factor 24.1%, Free R-factor 26.5% 2.4A csf1-csf1r-7 3 5 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 4 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 13 15 direct interaction direct interaction Fig. 1A csf1-csf1r-8 2 4 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 5 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 20 18 direct interaction direct interaction Fig. 1B csf1-csf1r-9 2 5 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 4 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 23 25 direct interaction direct interaction Fig. 1B