lateral-open conformation of the wild-type BAM complex (BamABCDE) bound to a bactericidal Fab fragment

2024-11-20 REL PDBe PDBe PDBe 2021-01-29 2021-06-02 2021-06-02 2024-11-20 Medical Research Council (MRC, United Kingdom) MR/P018491/1 United Kingdom Wellcome Trust 108466/Z/15/Z United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/M011151/1 United Kingdom Wellcome Trust 222373/Z/21/Z United Kingdom Wellcome Trust 105220/Z/14/Z United Kingdom Research Foundation - Flanders (FWO) G0G0818N Belgium Royal Society RSRP/R1/211057 United Kingdom lateral-open conformation of the wild-type BAM complex (BamABCDE) bound to a bactericidal Fab fragment Iadanza MG Outer membrane protein assembly, beta-barrel, Gram negative bacteria, protein foldase, MEMBRANE PROTEIN White P Haysom SF Iadanza MG Higgins AJ Machin JM Whitehouse JM Horne JE Schiffrin B Carpenter-Platt C Calabrese AN Storek KM Rutherford ST Brockwell DJ Ranson NA Radford SE The role of membrane destabilisation and protein dynamics in BAM catalysed OMP folding. Nat Commun UK 12 4174 4174 2021 34234105 doi:10.1038/s41467-021-24432-x 2041-1723 EMD-12232 other EM volume

Lateral-closed conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) by cryoEM

EMD-12262 other EM volume

Lateral-open conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) by cryoEM

EMD-12263 other EM volume

Lateral-open conformation of the POTRA-locked BAM complex by cryoEM

EMD-12271 other EM volume

Lateral-open conformation of the lid-locked BAM complex bound by a bactericidal Fab fragment

7nd0 FULLOVERLAP wild-type beta-barrel assembly machinery (BAM) complex (BamABCDE) bound by a bactericidal Fab fragment wild-type beta-barrel assembly machinery (BAM) complex (BamABCDE) bound by a bactericidal Fab fragment 0 1 2 3 4 5 6 7 Escherichia coli (strain K12) K12 0.048 wild-type beta-barrel assembly machinery (BAM) complex (BamABCDE) 1 1 2 3 4 5 Escherichia coli (strain K12) K12 Light and heavy chains of bactericidal Fab fragment Fab1 1 6 7 Homo sapiens Outer membrane protein assembly factor BamA Escherichia coli K-12 0.090643383 1 Escherichia coli BL21(DE3) LEVO MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRD GDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPR NRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNI DSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYP RVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDT DTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTV DGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSD QDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDG LGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFIT PTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAE QFQFNIGKTW P0A940 Outer membrane protein assembly factor BamB Escherichia coli K-12 0.041918945 1 Escherichia coli BL21(DE3) LEVO MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGL VKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDG LVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQS DLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITR P77774 Outer membrane protein assembly factor BamC Escherichia coli K-12 0.036875277 1 Escherichia coli BL21(DE3) LEVO MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKAL DIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGR YQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFID PKGHTLTQSQNDALVAVFQAAFSK P0A903 Outer membrane protein assembly factor BamD Escherichia coli K-12 0.027858349999999997 1 Escherichia coli BL21(DE3) LEVO MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYY KNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYT TDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA NSSNT P0AC02 Outer membrane protein assembly factor BamE Escherichia coli K-12 0.013530256 1 Escherichia coli BL21(DE3) LEVO MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQ PGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHHHHH P0A937 Fab1 heavy chain Homo sapiens 0.024501666 1 Escherichia coli LEVO EVQLVESGGGLVQPGRSLKLSCVASRFTFSNYGMNWIRQTPGKGLEWVAYIGSTSSHIYYAETVKGRFTISRDNAKNTLY LQMTGLRSEDTALYYCVGHVRKLGAFFDYWGQGAMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT Fab1 light chain Homo sapiens 0.023642214999999998 1 Escherichia coli LEVO DIQMTQSPASLSASLGETVTIECRASEDIHSRLAWYQQKPGKSPQLLIYNANSLHTGVPSRFSGSGSGTQFSLKINSLQS EDVASYFCLQYYNYPPYTFGAGAKLELRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC singleParticle particle 3.3 8.0 20.0 Tris-HCl Tris 150.0 NaCl sodium chloride 0.05 DDM n-dodecyl-beta-D-maltoside UltrAuFoil R2/2 GOLD 200 GLOW DISCHARGE

grids glow discharged for 60 sec at 20 mA in a GlowQube Plus

ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.75 3.25 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 74.9 GATAN K2 SUMMIT (4k x 4k) COUNTING 59.8 GATAN K2 SUMMIT (4k x 4k) COUNTING 60.9 1 703997

Initial model generated by stochastic gradient descent from the cleaned particle stack using RELION 3.0

5.2 FSC 0.143 CUT-OFF RELION 3.0 half maps from non-uniform refinement were postprocessed in RELION 3.0 cryoSPARC 2.2.0 final refinement used the non-uniform refinement in cryoSPARC 131853 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD cryoSPARC 2.2.0 final refinement used the non-uniform refinement in cryoSPARC RELION 3.0 emd_12272.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 372.75003 372.75003 372.75003 90.0 90.0 90.0 X Y Z -0.013149768 0.03905881 0.00010949919 0.001071387 1.065 1.065 1.065 0.011 AUTHOR ::::EMDATABANK.org::::EMD-12272:::: Postprocessed masked map of the BAM (BamABCDE) complex bound by a bactericidal Fab fragment 5LJO A 24-806 PDB experimental model 5EKQ A 687-700 PDB experimental model 5LJO B PDB experimental model 5LJO C PDB experimental model 5LJO D PDB experimental model 5LJO E PDB experimental model 7BM5 H PDB experimental model 7BM5 L PDB experimental model FLEXIBLE FIT

The starting BAM model was created from 5LJO (lateral-open BAM-WT cryoEM structure) with BamA residues 687-700 replaced by those from 5EKQ (crystal structure of BamACDE in a lateral-open conformation). This and 7BM5 (Fab1 crystal structure) were rigid fitted into the BAM-WT Fab1 complex electron density in UCSF Chimera. Molecular dynamics based flexible fitting was then set up in VMD and run in NAMD to fit the structures into the density. The resulting structure was finally real-space refined in phenix to generate the final model.

REAL 183.0 emd_12272_msk_1.map emd_12272_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 374.50003 374.50003 374.50003 90.0 90.0 90.0 X Y Z -0.014697556 0.03482385 -0.000003852712 0.0020662074 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::EMD-12272:::: Halfmap 1 from non-uniform refinement (cryoSPARC 2.2.0) of the polished particle stack emd_12272_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 374.50003 374.50003 374.50003 90.0 90.0 90.0 X Y Z -0.013881842 0.032244664 -0.000004240526 0.002072116 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::EMD-12272:::: Halfmap 2 from non-uniform refinement (cryoSPARC 2.2.0) of the polished particle stack