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

2024-10-16 REL PDBe PDBe PDBe 2021-01-22 2021-06-02 2021-06-02 2024-10-16 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-closed conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) by cryoEM Haysom SF 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 7bnq FULLOVERLAP beta-barrel assembly machinery (BAM) complex (BamABCDE) beta-barrel assembly machinery (BAM) complex (BamABCDE) 0 1 2 3 4 5 Escherichia coli (strain K12) K12 0.203 Outer membrane protein assembly factor BamA Escherichia coli (strain K12) K12 0.090601352 1 Escherichia coli BL21(DE3) LEVO MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRD GDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPR NRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNI DSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYP RVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDT DTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTCSGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTV DGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSD QDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDG LGGKEMPFYENFYAGGSSTVRGFQCNTIGPKAVYFPHQASNYDPDYDYESATQDGAKDLSKSDDAVGGNAMAVASLEFIT PTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAE QFQFNIGKTW P0A940 Outer membrane protein assembly factor BamB Escherichia coli (strain K12) K12 0.041918945 1 Escherichia coli BL21(DE3) LEVO MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGL VKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDG LVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQS DLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITR P77774 Outer membrane protein assembly factor BamC Escherichia coli (strain K12) K12 0.036875277 1 Escherichia coli BL21(DE3) LEVO MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKAL DIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGR YQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFID PKGHTLTQSQNDALVAVFQAAFSK P0A903 Outer membrane protein assembly factor BamD Escherichia coli (strain K12) K12 0.027858349999999997 1 Escherichia coli BL21(DE3) LEVO MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYY KNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYT TDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA NSSNT P0AC02 Outer membrane protein assembly factor BamE Escherichia coli (strain K12) K12 0.013530256 1 Escherichia coli BL21(DE3) LEVO MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQ PGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHHHHH P0A937 singleParticle particle 3.3 8.0 50.0 Tris-HCl Tris 150.0 NaCl sodium chloride 0.05 DDM n-dodecyl-beta-D-maltoside Quantifoil COPPER 400 GLOW DISCHARGE ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 3.0 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 49.7 1 793444

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

BACK PROJECTION 4.1 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 160118 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD cryoSPARC 2.2.0 final refinement used the non-uniform refinement in cryoSPARC RELION 3.0 emd_12232.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 321.00003 321.00003 321.00003 90.0 90.0 90.0 X Y Z -1.2526962 2.2841878 0.0037964298 0.043703213 1.07 1.07 1.07 0.503 AUTHOR ::::EMDATABANK.org::::EMD-12232:::: Postprocessed masked map of the lateral-closed conformation of a lid-locked BAM complex 5D0O A PDB experimental model 5D0O B PDB experimental model 5D0O C PDB experimental model 5D0O D PDB experimental model 5D0O E PDB experimental model OTHER REAL 103.0 emd_12232_msk_1.map emd_12232_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 321.00003 321.00003 321.00003 90.0 90.0 90.0 X Y Z -1.1056515 1.2666156 0.0023165639 0.1332232 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::EMD-12232:::: Halfmap 2 from non-uniform refinement (cryoSPARC 2.2.0) of the polished particle stack emd_12232_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 321.00003 321.00003 321.00003 90.0 90.0 90.0 X Y Z -1.2161366 1.361301 0.002342316 0.13326536 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::EMD-12232:::: Halfmap 1 from non-uniform refinement (cryoSPARC 2.2.0) of the polished particle stack