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/ Structural basis of outer membrane protein biogenesis in bacteria. Structural basis of outer membrane protein biogenesis in bacteria. J. Biol. Chem. (0021-9258) 2011 imex curation Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro crosslink cross-linking study crosslink predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Structural basis of outer membrane protein biogenesis in bacteria. Structural basis of outer membrane protein biogenesis in bacteria. J. Biol. Chem. (0021-9258) 2011 imex curation Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions ecoli Escherichia coli (strain K12) saxs x ray scattering saxs predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Structural basis of outer membrane protein biogenesis in bacteria. Structural basis of outer membrane protein biogenesis in bacteria. J. Biol. Chem. (0021-9258) 2011 imex curation Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions ecoli Escherichia coli (strain K12) comigration in sds comigration in sds page comigration in sds predetermined predetermined participant predetermined Albrecht R., Zeth K. gel filtrations used to separate proteins after crosslinking with glutaraldehyde Kornelius.Zeth@tuebingen.mpg.de Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Structural basis of outer membrane protein biogenesis in bacteria. Structural basis of outer membrane protein biogenesis in bacteria. J. Biol. Chem. (0021-9258) 2011 imex curation Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions ecoli Escherichia coli (strain K12) x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Structural basis of outer membrane protein biogenesis in bacteria. Structural basis of outer membrane protein biogenesis in bacteria. J. Biol. Chem. (0021-9258) 2011 imex curation Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro pull down pull down predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation Structural basis of outer membrane protein biogenesis in bacteria. Structural basis of outer membrane protein biogenesis in bacteria. J. Biol. Chem. (0021-9258) 2011 imex curation Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions ecoli Escherichia coli (strain K12) molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de Accepted 2012-DEC-12 by MGT 18-Dec-2012: Contacted by IntAct-Help. J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation bamb_ecoli Outer membrane protein assembly factor BamB bamB yfgL JW2496 b2512 protein protein ecoli Escherichia coli (strain K12) MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITR DIP protein P77774 original sequence version: 112 DIP protein P77774 original sequence version: 127 DIP protein P77774 original sequence version: 128 BCFAFA061A486B31 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 bama_ecoli Outer membrane protein assembly factor BamA bamA Omp85 yaeT yzzN yzzY JW0172 b0177 protein protein ecoli Escherichia coli (strain K12) MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW DIP protein P0A940 original sequence version: 84 DIP protein P0A940 original sequence version: 102 DIP protein P0A940 original sequence version: 103 DDCE4C6D341664EB 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 bame_ecoli Outer membrane protein assembly factor BamE bamE smpA b2617 JW2598 protein protein ecoli Escherichia coli (strain K12) MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGN DIP protein P0A937 original sequence version: 75 DIP protein P0A937 original sequence version: 87 DIP protein P0A937 original sequence version: 88 CFD8840C014AA0A2 bame hexamer 1 11 unspecified role unspecified role neutral component neutral component 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 ecoli Escherichia coli (strain K12) physical association physical association Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bamabd 5 9 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 7 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 ecoli Escherichia coli (strain K12) physical association physical association Fig. 1b bama-bamd 5 8 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role prey prey 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Fig. 1b bamb-bama 5 7 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 ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) direct interaction direct interaction Fig. 1b bamc-bamc 2 10 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 ecoli Escherichia coli (strain K12) 10 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Fig. 4e 2yh5: 1.25 A 2yh6: 1.55 A 2yh5: R = 0.15 Rworking = 0.15 Rfree = 0.18 2yh6: R = 0.2 Rworking = 0.19 Rfree = 0.23 dimer of 2 separately-expressed domains of BamC (P0A903) bame truncated 6 11 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 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 physical association physical association Fig. 6a, c bame-bame 4 11 unspecified role unspecified role neutral component neutral component 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 direct interaction direct interaction Fig. 5 Fig. 5 shows homohexamer made from 3 sets of homodimers, PDB entry referes to dimers in experiment and hexamers in quaternary structure R = 0.18 Rworking = 0.18 Rfree = 0.23 1.8 A homohexamer made up of three sets of homodimers bame hexamer 6 11 unspecified role unspecified role neutral component neutral component 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 physical association physical association Fig. 6b, d part of Bam/OMP complex bame truncated hexamer 1 11 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 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 ecoli Escherichia coli (strain K12) physical association physical association Fig. 6c bamb-tetramer 6 7 unspecified role unspecified role unspecified role unspecified role 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 physical association physical association Fig. 3b bamb-hexamer 6 7 unspecified role unspecified role unspecified role unspecified role 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 physical association physical association Fig. 3b bamc n-terminal dimer 4 10 unspecified role unspecified role unspecified role unspecified role n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain direct interaction direct interaction Suppl. Fig. S4a R = 0.2 Rworking = 0.19 Rfree = 0.23 1.55 A dimer of N-terminal domain bame tetramer 1 11 unspecified role unspecified role neutral component neutral component 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 ecoli Escherichia coli (strain K12) physical association physical association Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame trimer 1 11 unspecified role unspecified role neutral component neutral component 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 ecoli Escherichia coli (strain K12) physical association physical association Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame dimer 3 11 unspecified role unspecified role neutral component neutral component 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 physical association physical association Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame truncated tetramer 1 11 unspecified role unspecified role neutral component neutral component 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association Fig. 6c bame truncated trimer 1 11 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 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 ecoli Escherichia coli (strain K12) physical association physical association Fig. 6c bame truncated dimer 3 11 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 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 physical association physical association Fig. 6c bamd dimer 1 8 unspecified role unspecified role unspecified role unspecified role ecoli Escherichia coli (strain K12) physical association physical association Fig. 6e Addition of Hia-1 peptide facilitates dimerisation of C-terminally truncated BamD (region not given!) but not full lengths BamD. Addition of peptide Hia-2 didn't seem to make any difference. The gel is difficult to read and there is no discussion of it in the Results or Discussion sections. bame dimer 1 11 unspecified role unspecified role neutral component neutral component 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 ecoli Escherichia coli (strain K12) physical association physical association Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame truncated dimer 1 11 unspecified role unspecified role neutral component neutral component 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association Fig. 6c