DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ yan-2017-3 ecoli Escherichia coli (strain K12) comigration in sds comigration in sds page comigration in sds experimental particp experimental participant identification experimental particp Yan Z., Yin M., Xu D., Zhu Y., Li X. zhuyongqun@zju.edu.cn, lixueming@tsinghua.edu.cn Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation yan-2017-1 ecoli Escherichia coli (strain K12) 3d-em 3D electron microscopy 3D-EM electron tomog experimental particp experimental participant identification experimental particp Yan Z., Yin M., Xu D., Zhu Y., Li X. zhuyongqun@zju.edu.cn, lixueming@tsinghua.edu.cn Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation yan-2017-2 ecoli Escherichia coli (strain K12) molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column experimental particp experimental participant identification experimental particp Yan Z., Yin M., Xu D., Zhu Y., Li X. zhuyongqun@zju.edu.cn, lixueming@tsinghua.edu.cn Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation gspd_vibch Secretin GspD epsD Cholera toxin secretion protein EpsD General secretion pathway protein D Type II secretion system protein D VC_2733 protein protein vibch Vibrio cholerae MKYWLKKSSWLLAGSLLSTPLAMANEFSASFKGTDIQEFINIVGRNLEKTIIVDPSVRGKVDVRSFDTLNEEQYYSFFLSVLEVYGFAVVEMDNGVLKVIKSKDAKTSAIPVLSGEERANGDEVITQVVAVKNVSVRELSPLLRQLIDNAGAGNVVHYDPANIILITGRAAVVNRLAEIIRRVDQAGDKEIEVVELNNASAAEMVRIVEALNKTTDAQNTPEFLKPKFVADERTNSILISGDPKVRERLKRLIKQLDVEMAAKGNNRVVYLKYAKAEDLVEVLKGVSENLQAEKGTGQPTTSKRNEVMIAAHADTNSLVLTAPQDIMNAMLEVIGQLDIRRAQVLIEALIVEMAEGDGINLGVQWGSLESGSVIQYGNTGASIGNVMIGLEEAKDTTQTKAVYDTNNNFLRNETTTTKGDYTKLASALSSIQGAAVSIAMGDWTALINAVSNDSSSNILSSPSITVMDNGEASFIVGEEVPVITGSTAGSNNDNPFQTVDRKEVGIKLKVVPQINEGNSVQLNIEQEVSNVLGANGAVDVRFAKRQLNTSVMVQDGQMLVLGGLIDERALESESKVPLLGDIPLLGQLFRSTSSQVEKKNLMVFIKPTIIRDGVTADGITQRKYNYIRAEQLFRAEKGLRLLDDASVPVLPKFGDDRRHSPEIQAFIEQMEAKQ 3D77B891A59E6223 gspd_ecoli Putative secretin GspD Putative general secretion pathway protein D Putative type II secretion system protein D gspD yheF b3325 JW5707 protein protein ecoli Escherichia coli (strain K12) MKGLNKITCCLLAALLMPCAGHAENEQYGANFNNADIRQFVEIVGQHLGKTILIDPSVQGTISVRSNDTFSQQEYYQFFLSILDLYGYSVITLDNGFLKVVRSANVKTSPGMIADSSRPGVGDELVTRIVPLENVPARDLAPLLRQMMDAGSVGNVVHYEPSNVLILTGRASTINKLIEVIKRVDVIGTEKQQIIHLEYASAEDLAEILNQLISESHGKSQMPALLSAKIVADKRTNSLIISGPEKARQRITSLLKSLDVEESEEGNTRVYYLKYAKATNLVEVLTGVSEKLKDEKGNARKPSSSGAMDNVAITADEQTNSLVITADQSVQEKLATVIARLDIRRAQVLVEAIIVEVQDGNGLNLGVQWANKNVGAQQFTNTGLPIFNAAQGVADYKKNGGITSANPAWDMFSAYNGMAAGFFNGDWGVLLTALASNNKNDILATPSIVTLDNKLASFNVGQDVPVLSGSQTTSGDNVFNTVERKTVGTKLKVTPQVNEGDAVLLEIEQEVSSVDSSSNSTLGPTFNTRTIQNAVLVKTGETVVLGGLLDDFSKEQVSKVPLLGDIPLVGQLFRYTSTERAKRNLMVFIRPTIIRDDDVYRSLSKEKYTRYRQEQQQRIDGKSKALVGSEDLPVLDENTFNSHAPAPSSR epsd-epsd-3 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Leu508Asp L484D mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Leu508Asp L484D mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7b (L484D lane) epsd-epsd-4 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Val510Asp V486D mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Val510Asp V486D mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7b (V486D lane) epsd-epsd-5 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Leu522Asp L498D mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Leu522Asp L498D mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7b (L498D lane) epsd-epsd-6 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Ile524Glu I500E mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Ile524Glu I500E mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7b (I500E lane) epsd-epsd-7 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Ile605Glu I581E mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Ile605Glu I581E mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7b (I581E lane) epsd-epsd-8 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Gly477Ala G477A mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Gly477Ala G453A mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7c (G453A lane) epsd-epsd-9 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Gly505Ala G481A mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Gly505Ala G481A mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7c (G481A lane) epsd-epsd-10 3547158 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified P45779:p.[Gly477Ala;Gly505Ala] G453A,G481A mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.[Gly477Ala;Gly505Ala] G453A,G481A mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 7c (G453A&G481A lane) gspd-6 3547159 N/A 3547162 structure determination identification by structure determination identification by structure determination structure determination ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 15.0 direct interaction direct interaction false false false Figure1, Table1, Supplementary Figure 2 epsd-11 3547159 N/A 3547161 structure determination identification by structure determination identification by structure determination structure determination ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified p.Gly371_Ala393del 371-393 mutation mutation certain certain sequence position certain certain certain sequence position certain false strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 15.0 direct interaction direct interaction false false false Figure1, Table1, Supplementary Figure 2 epsd-1 3547159 N/A 3547161 structure determination identification by structure determination identification by structure determination structure determination ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P45779:p.Gly477Ala G453A mutation mutation certain certain sequence position certain certain certain sequence position certain false The mutation occurs on the 477th position on the original sequence (the sequence used in this paper starts from the 24th AA). binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 15.0 direct interaction direct interaction false false false Figure1, Table1, Supplementary Figure 2 epsd-12 3547159 N/A 3547161 structure determination identification by structure determination identification by structure determination structure determination ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 15.0 direct interaction direct interaction false false false Figure1, Table1, Supplementary Figure 2 gspd-gspd-2 3547160 N/A 3547162 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547162 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 1c epsd-epsd-2 3547160 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 1e epsd-epsd-1 3547160 N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547161 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 1f gspd-gspd-1 3547160 N/A 3547162 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3547162 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined ms participant Identification by mass spectrometry ms participant unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified strep tag strep tag strep tag strep tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 1d