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/ albrecht-2011-7 Structural basis of outer membrane protein biogenesis in bacteria. in vitro In vitro crosslink cross-linking study crosslink predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation albrecht-2011-1 Structural basis of outer membrane protein biogenesis in bacteria. 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 J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation albrecht-2011-2 Structural basis of outer membrane protein biogenesis in bacteria. in vitro In vitro pull down pull down predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation albrecht-2011-4 Structural basis of outer membrane protein biogenesis in bacteria. 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 J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation albrecht-2011-5 Structural basis of outer membrane protein biogenesis in bacteria. 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 J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation albrecht-2011-3 Structural basis of outer membrane protein biogenesis in bacteria. ecoli Escherichia coli (strain K12) saxs x ray scattering saxs predetermined predetermined participant predetermined Albrecht R., Zeth K. Kornelius.Zeth@tuebingen.mpg.de J. Biol. Chem. (0021-9258) 2011 Only protein-protein interactions imex curation bame_ecoli Outer membrane protein assembly factor BamE bamE smpA b2617 JW2598 protein protein ecoli Escherichia coli (strain K12) MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGN bamd_ecoli Outer membrane protein assembly factor BamD bamD yfiO JW2577 b2595 protein protein ecoli Escherichia coli (strain K12) MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT bamb_ecoli Outer membrane protein assembly factor BamB bamB yfgL JW2496 b2512 protein protein ecoli Escherichia coli (strain K12) MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITR bama_ecoli Outer membrane protein assembly factor BamA bamA Omp85 yaeT yzzN yzzY JW0172 b0177 protein protein ecoli Escherichia coli (strain K12) MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW bamc_ecoli Outer membrane protein assembly factor BamC bamC dapX nlpB JW2462 b2477 protein protein ecoli Escherichia coli (strain K12) MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK bame hexamer 1331039 n/a 1331045 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 false ecoli Escherichia coli (strain K12) Stoichiometry: 6.0 physical association physical association false false false Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame truncated hexamer 1331039 n/a 1331045 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 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 ecoli Escherichia coli (strain K12) Stoichiometry: 6.0 physical association physical association false false false Fig. 6c bame tetramer 1331039 n/a 1331045 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 false ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 physical association physical association false false false Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame trimer 1331039 n/a 1331045 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 false ecoli Escherichia coli (strain K12) Stoichiometry: 3.0 physical association physical association false false false Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame truncated tetramer 1331039 n/a 1331045 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 false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 physical association physical association false false false Fig. 6c bame truncated trimer 1331039 n/a 1331045 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 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 ecoli Escherichia coli (strain K12) Stoichiometry: 3.0 physical association physical association false false false Fig. 6c bame dimer 1331039 n/a 1331045 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 false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 physical association physical association false false false Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame truncated dimer 1331039 n/a 1331045 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 false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 physical association physical association false false false Fig. 6c bamd dimer 1331039 n/a 1331046 unspecified role unspecified role unspecified role unspecified role ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 physical association physical association false false false 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 truncated 1331040 n/a 1331045 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 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 Stoichiometry: 4.0 physical association physical association false false false Fig. 6a, c bame hexamer 1331040 n/a 1331045 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 false Stoichiometry: 6.0 physical association physical association false false false Fig. 6b, d part of Bam/OMP complex bamb-tetramer 1331040 n/a 1331047 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 false Stoichiometry: 4.0 physical association physical association false false false Fig. 3b bamb-hexamer 1331040 n/a 1331047 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 false Stoichiometry: 6.0 physical association physical association false false false Fig. 3b bamabd 1331041 n/a 1331048 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1331046 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1331047 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 ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 1b bama-bamd 1331041 n/a 1331046 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1331048 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 false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 1b bamb-bama 1331041 n/a 1331047 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 ecoli Escherichia coli (strain K12) n/a 1331048 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 1b bame-bame 1331042 n/a 1331045 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 false Stoichiometry: 2.0 direct interaction direct interaction false false false 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 bamc n-terminal dimer 1331042 n/a 1331049 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 false direct interaction direct interaction false false false Suppl. Fig. S4a R = 0.2 Rworking = 0.19 Rfree = 0.23 1.55 A dimer of N-terminal domain bame dimer 1331043 n/a 1331045 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 false Stoichiometry: 2.0 physical association physical association false false false Fig. 6d gluaraldehyde chross-linking enables oligomerisation up to hexamers, also shown by crystallization (see Expt. 3) bame truncated dimer 1331043 n/a 1331045 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 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 Stoichiometry: 2.0 physical association physical association false false false Fig. 6c bamc-bamc 1331044 n/a 1331049 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 ecoli Escherichia coli (strain K12) n/a 1331049 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 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)