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/ Crystal structure of β-barrel assembly machinery BamCD protein complex. Crystal structure of β-barrel assembly machinery BamCD protein complex. J. Biol. Chem. (0021-9258) 2011 imex curation Kim K.H., Aulakh S., Paetzel M. kkim@sfu.ca, ska16@sfu.ca, mpaetzel@sfu.ca 19-Sept-2012: Contacted by IntAct-Help. Although the experiment is done with a cell lysate, the interaction type is direct because the authors prove it with two other experiments: 1. They check the size of the purified complex by gel filtration chromatography in-line with a multiangle light-scattering system. They show that the molecular weight of the purified complex corresponds to the molecular weight of the two proteins together (BamC and BamD). 2. They perform a protein gel electrophoresis with the purified complex and show the existence of only two proteins in the complex: BamC and BamD. They use the corresponding molecular weights for their identification. 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 Kim K.H., Aulakh S., Paetzel M. kkim@sfu.ca, ska16@sfu.ca, mpaetzel@sfu.ca Accepted 2012-JUL-24 by ORCHARD 19-Sept-2012: Contacted by IntAct-Help. Although the experiment is done with a cell lysate, the interaction type is direct because the authors prove it with two other experiments: 1. They check the size of the purified complex by gel filtration chromatography in-line with a multiangle light-scattering system. They show that the molecular weight of the purified complex corresponds to the molecular weight of the two proteins together (BamC and BamD). 2. They perform a protein gel electrophoresis with the purified complex and show the existence of only two proteins in the complex: BamC and BamD. They use the corresponding molecular weights for their identification. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Crystal structure of β-barrel assembly machinery BamCD protein complex. Crystal structure of β-barrel assembly machinery BamCD protein complex. J. Biol. Chem. (0021-9258) 2011 imex curation Kim K.H., Aulakh S., Paetzel M. kkim@sfu.ca, ska16@sfu.ca, mpaetzel@sfu.ca 19-Sept-2012: Contacted by IntAct-Help. Although the experiment is done with a cell lysate, the interaction type is direct because the authors prove it with two other experiments: 1. They check the size of the purified complex by gel filtration chromatography in-line with a multiangle light-scattering system. They show that the molecular weight of the purified complex corresponds to the molecular weight of the two proteins together (BamC and BamD). 2. They perform a protein gel electrophoresis with the purified complex and show the existence of only two proteins in the complex: BamC and BamD. They use the corresponding molecular weights for their identification. Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by comassie molecular weight estimation by coomasie staining weight by comassie Kim K.H., Aulakh S., Paetzel M. kkim@sfu.ca, ska16@sfu.ca, mpaetzel@sfu.ca Accepted 2012-JUL-24 by ORCHARD 19-Sept-2012: Contacted by IntAct-Help. Although the experiment is done with a cell lysate, the interaction type is direct because the authors prove it with two other experiments: 1. They check the size of the purified complex by gel filtration chromatography in-line with a multiangle light-scattering system. They show that the molecular weight of the purified complex corresponds to the molecular weight of the two proteins together (BamC and BamD). 2. They perform a protein gel electrophoresis with the purified complex and show the existence of only two proteins in the complex: BamC and BamD. They use the corresponding molecular weights for their identification. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation bamc_ecoli Outer membrane protein assembly factor BamC bamC dapX nlpB JW2462 b2477 protein protein ecoli Escherichia coli (strain K12) MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK DIP protein P0A903 original sequence version: 95 DIP protein P0A903 original sequence version: 96 49991F277D9D923C bamd_ecoli Outer membrane protein assembly factor BamD bamD yfiO JW2577 b2595 protein protein ecoli Escherichia coli (strain K12) MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT DIP protein P0AC02 original sequence version: 70 DIP protein P0AC02 original sequence version: 82 DIP protein P0AC02 original sequence version: 83 91D0A25E69248C49 bamc-bamd 2 3 biological role biological role neutral component neutral component tag 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 region sufficient to bind sufficient binding region sufficient to bind full dna sequence full identification by DNA sequencing full dna sequence certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 4 biological role biological role neutral component neutral component tag 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 region sufficient to bind sufficient binding region sufficient to bind full dna sequence full identification by DNA sequencing full dna sequence certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 8 11 direct interaction direct interaction FIGURE 1. Formation of the BamCD complex. bamc-bamd-1 2 4 biological role biological role neutral component neutral component tag 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 region sufficient to bind sufficient binding region sufficient to bind full dna sequence full identification by DNA sequencing full dna sequence certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 3 biological role biological role neutral component neutral component region required to bind necessary binding region required to bind full dna sequence full identification by DNA sequencing full dna sequence certain certain sequence position certain certain certain sequence position certain tag 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 ecoli Escherichia coli (strain K12) 17 15 direct interaction direct interaction FIGURE 1. Formation of the BamCD complex bamc-bamd-2 1 4 biological role biological role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind full dna sequence full identification by DNA sequencing full dna sequence certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 3 biological role biological role neutral component neutral component region required to bind necessary binding region required to bind full dna sequence full identification by DNA sequencing full dna sequence certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 23 21 direct interaction direct interaction Figure 2, Figure 3 Although the full-length BamCD complex was used for crystallization, BamC was cleaved to a smaller fragment corresponding to BamCUN (Asp28–Ala217) in the crystallization drop during incubation. BamC has been previously shown to be susceptible to degradation in the linker region connecting the N- and C-terminal domains. 2.9A R-Value: 0.181 (obs.), R-Free: 0.243