8BWC

E. coli BAM complex (BamABCDE) wild-type

• PDB DOI: https://doi.org/10.2210/pdb8BWC/pdb
• EM Map EMD-16282: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3), Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-12-06 Released: 2023-05-24 
• Deposition Author(s): Machin, J.M., Radford, S.E., Ranson, N.A.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells.

Haysom, S.F., Machin, J., Whitehouse, J.M., Horne, J.E., Fenn, K., Ma, Y., El Mkami, H., Bohringer, N., Schaberle, T.F., Ranson, N.A., Radford, S.E., Pliotas, C.

(2023) Angew Chem Int Ed Engl 62: e202218783-e202218783

• PubMed: 37162386 
• DOI: https://doi.org/10.1002/anie.202218783
• Primary Citation of Related Structures:  
  8BVQ, 8BWC


• PubMed Abstract: 
  

  The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.

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Organizational Affiliation: 

Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 200.23 kDa 
• Atom Count: 11,266 
• Modelled Residue Count: 1,442 
• Deposited Residue Count: 1,813 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	A	790	Escherichia coli	Mutation(s): 0  Gene Names:  bamA, yaeT, A5U30_000296, A6592_02945, A8499_001882, A9X72_20365, AAG43_001505, ACN68_08270, ACN81_28495, ACU57_18535, AF998_001683, AM464_17685, APX88_24870, AT335_002559, AT845_002198, AW118_17900, AWP47_05630, B6R12_000956, B6R15_000220, B6R31_002460, B6R48_000717, B6R87_000718, BANRA_00651, BANRA_01136, BEA19_03425, BER14_07740, BF481_003681, BG944_001864, BGM66_002013, BHS81_00690, BJI68_15680, BJJ90_21320, BK292_13710, BK383_20200, BKL28_001074, BLM69_001467, BMT49_02215, BMT50_03970, BMT91_01325, BN17_46001, BO068_002867, BOH76_17675, BON63_15405, BON64_03425, BON65_09470, BON66_02910, BON67_09950, BON68_19005, BON69_16435, BON70_27195, BON71_14840, BON72_09420, BON73_05360, BON74_02620, BON75_17190, BON76_15510, BON77_21970, BON78_08335, BON79_15615, BON80_16360, BON81_06815, BON82_14505, BON83_24810, BON84_04065, BON87_26650, BON88_11825, BON89_11070, BON90_22375, BON92_02795, BON93_03895, BON94_19435, BON95_12990, BON96_17170, BON98_18140, BR158_000492, BRV02_001577, BTB68_000231, BTQ06_06530, BvCmsF30A_01249, BvCmsHHP056_04085, BvCmsKKP061_01626, BVL39_02145, BXT93_00750, C0P57_001486, C1Q91_003240, C2121_002944, C2M16_10840, C2R31_000619, C2U48_09565, C3F40_12200, C5N07_08620, C5Y87_12615, C9114_06985, C9160_13545, C9E67_25165, C9Z68_04825, CA593_02825, CCS08_22545, CCV12_001992, CDC27_24730, CDL36_07950, CF22_003987, CG831_000812, CIG67_16620, CO706_23095, CQ986_003586, CR538_20600, CR628_003260, CTR35_003026, CV83915_01397, CWS33_09660, CX938_000225, CXJ73_002511, CY655_00940, D0X26_09375, D1912_21110, D1H34_004224, D3G36_16715, D3Y67_16445, D4N09_06760, D4U49_05910, D9D77_16570, D9E34_01065, D9E49_02105, D9J61_11550, DAH17_03105, DAH18_22205, DAH19_12870, DAH20_13860, DAH21_22225, DAH22_03605, DAH23_11155, DAH24_11225, DAH25_12780, DAH26_11170, DAH27_18735, DAH28_17975, DAH29_14730, DAH30_10570, DAH31_15650, DAH32_15150, DAH33_22250, DAH34_04145, DAH35_21475, DAH36_21050, DAH37_16290, DAH38_20975, DAH40_22075, DAH41_15665, DAH42_01610, DAH43_04070, DAH45_06290, DAH46_02585, DAH47_00130, DAH48_03820, DAH49_04075, DAH50_07015, DD762_01135, DEN86_04025, DEN87_21110, DEN88_17015, DEN89_20325, DEN90_18665, DEN91_15525, DEN92_14715, DEN93_18270, DEN94_16145, DEN95_12205, DEN96_06230, DEN97_04385, DEN98_04390, DEN99_03155, DEO00_05230, DEO01_06055, DEO02_09495, DEO03_16425, DEO04_22130, DEO05_22000, DEO06_22645, DEO07_22470, DEO08_20705, DEO09_21855, DEO10_22115, DEO11_22010, DEO13_08600, DEO14_11200, DEO15_08380, DEO17_19865, DEO18_03450, DEO19_04170, DEO20_19760, DIV22_06310, DM870_23205, DN627_10205, DNQ45_10075, DNX30_02230, DRW19_04885, DS732_05815, DTL43_05880, DTL90_09775, DTM45_12675, DU321_03690, DXT69_01430, DXT70_16970, DXT71_01950, DXT73_18965, E0I42_19020, E2112_01200, E2113_05810, E2114_18200, E2115_17415, E2116_17440, E2117_05485, E2118_15330, E2119_15620, E2120_18160, E2121_14045, E2122_04495, E2123_15040, E2124_16725, E2125_18030, E2127_15050, E2128_01390, E2129_02820, E2130_17625, E2131_12100, E2132_15165, E2133_09940, E2134_12015, E2135_11675, E2136_14045, E2646_16120, E3O05_11515, E4K51_05750, E4T14_02285, E4T84_08860, E5H86_15850, E5M02_17400, E5P22_04130, E5P23_04750, E5P24_16165, E5P25_12900, E5P26_03475, E5P27_14125, E5P28_14015, E5P29_07840, E5P30_07230, E5P31_13525, E5P32_01600, E5P33_01100, E5P34_12070, E5P35_01145, E5P36_00555, E5P37_21230, E5P39_14350, E5P40_06990, E5P41_07170, E5P42_02575, E5P43_09410, E5P44_10415, E5P45_09040, E5P46_08190, E5P47_11175, E5P48_06230, E5P49_11800, E5P50_17540, E5P51_06990, E5P52_06800, E5S34_18420, E5S35_00130, E5S36_11165, E5S37_18815, E5S38_07550, E5S39_17385, E5S42_18205, E5S43_01760, E5S44_09525, E5S45_04825, E5S46_19575, E5S47_12360, E5S48_12815, E5S51_08320, E5S52_09495, E5S53_16295, E5S54_18365, E5S55_16285, E5S57_07225, E5S58_05565, E5S59_11205, E5S61_20105, E5S62_13815, E6C80_03245, E6D34_00950, EA239_13380, EA435_20340, EAI46_03605, EAN77_17385, EAX79_05520, EC1094V2_3674, EC95NR1_04363, ECs0179, ED648_00125, EHD79_10695, EI021_19885, EIA08_06365, EIZ93_07885, EKI52_10395, EL79_3697, EL80_3644, ELT16_21295, ELT17_01290, ELT20_04510, ELT21_15085, ELT22_08915, ELT23_12135, ELT24_18765, ELT25_21005, ELT26_05540, ELT27_04430, ELT28_17160, ELT29_02955, ELT30_18480, ELT31_08735, ELT32_04825, ELT33_15830, ELT34_19930, ELT35_06860, ELT36_13995, ELT38_13410, ELT39_20820, ELT40_02090, ELT41_02015, ELT44_21565, ELT45_20755, ELT46_21905, ELT48_12220, ELT49_18515, ELT50_04880, ELT52_04095, ELT55_19355, ELT56_04900, ELT58_11855, ELT59_17805, ELT60_20990, ELT61_17455, ELT63_15940, ELT72_19860, ELU07_12965, ELU82_16735, ELU83_06320, ELU85_21230, ELU88_20065, ELU89_12480, ELU90_03595, ELU91_18160, ELU94_15850, ELU95_07310, ELU97_22235, ELU98_09250, ELU99_07115, ELV00_10965, ELV01_05815, ELV02_21170, ELV03_21745, ELV04_21635, ELV07_04635, ELV08_10240, ELV09_11020, ELV10_05925, ELV11_07255, ELV12_07985, ELV13_13185, ELV15_10235, ELV16_14945, ELV20_03255, ELV21_07945, ELV22_16495, ELV23_20045, ELV26_20265, ELV28_04145, ELV29_15990, ELV40_17675, ELX48_04100, ELX61_13270, ELX66_06770, ELX68_15925, ELX69_11295, ELX76_14590, ELX79_12450, ELX85_10405, ELX96_04985, ELY02_13720, ELY31_21175, ELY32_08495, ELY39_01365, ELY41_06580, ELY48_16875, EN85_001940, EPS76_09925, ERS085406_00578, ERS139208_01237, EWK56_14925, EYV17_16485, EYV18_21785, F0L67_09105, F2N20_00125, F2N31_00125, F3N40_16060, F7F11_02035, F7N46_12575, F9413_16900, F9461_04780, F9B07_03480, F9V24_09540, F9X20_09395, FDM60_08780, FE584_15725, FE587_16410, FEJ01_15100, FFF58_06145, FHO90_19930, FIJ20_13935, FJQ40_14175, FKO60_12300, FOI11_012800, FOI11_22880, FPI65_00965, FPJ29_11720, FPS11_04890, FQF29_01490, FV293_02855, FVB16_04485, FWK02_04400, FY127_02905, FZC17_23605, FZN31_19945, FZU14_18300, G3565_18205, G3813_000507, G3V95_02420, G3W53_17975, G4A38_19380, G4A47_18815, G5603_21720, G7630_000814, G9448_10075, GAI66_14365, GAI89_16125, GAJ12_05920, GAJ26_21420, GF147_13240, GF699_14310, GFY34_15765, GIB53_10160, GJ11_00925, GJO56_09475, GKF66_15225, GKF89_14740, GNW61_11420, GNZ05_09785, GOP25_07210, GP711_09570, GP944_03110, GQM04_14355, GQM21_02740, GQN34_16145, GQW80_13555, GRC73_19630, GRW05_07735, GSM54_14470, GTP88_05365, GUC01_17920, GUI33_00125, H0O37_03390, H0O39_04955, H0O72_10145, H6Y26_004466, HEP30_016645, HEP34_000941, HHH44_003655, HI055_000768, HIE29_003111, HJQ60_000684, HJS37_001619, HJU54_003394, HKA49_001644, HL563_02695, HL601_07740, HLV18_20665, HLX92_18930, HLZ50_06920, HmCms169_00369, HMJ82_00130, HMU06_10015, HMV95_04545, HMW38_10535, HNC36_16200, HNC59_20385, HNC66_11645, HNC99_17465, HND12_10395, HV109_19340, HV209_01580, HVV39_17670, HVW04_10185, HVW19_15015, HVW43_11715, HVY77_20925, HVZ71_20360, HX136_20560, I6H01_17735, I6H02_18690, IFB95_000535, IH768_15425, IT029_001934, J0541_003907, J4S20_003219, JE86ST02C_01710, JE86ST05C_01740, JFD_01263, JNP96_05075, NCTC10082_01374, NCTC10089_04067, NCTC10090_02151, NCTC10429_04185, NCTC10865_05056, NCTC11112_03444, NCTC11181_01353, NCTC12950_04415, NCTC13127_05445, NCTC13148_05206, NCTC13216_02723, NCTC4450_07390, NCTC8008_03664, NCTC8009_07311, NCTC8621_04193, NCTC8959_04852, NCTC8960_01553, NCTC9037_04180, NCTC9073_03384, NCTC9111_04256, NCTC9706_01328, NCTC9775_02319, NCTC9777_00463, ND22_002541, RG28_03870, SAMEA3472044_04148, SAMEA3472056_00964, SAMEA3472147_00389, SAMEA3751407_04805, SAMEA3752557_00883, SAMEA3753106_03559, TUM18780_35950, WP4S18E07_36860, WR15_02370, XU56_000257 Membrane Entity: Yes
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12)) Explore P0A940  Go to UniProtKB:  P0A940

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamB	B	373	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: bamB, yfgL, b2512, JW2496 Membrane Entity: Yes
UniProt
Find proteins for P77774 (Escherichia coli (strain K12)) Explore P77774  Go to UniProtKB:  P77774

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamC	C	320	Escherichia coli	Mutation(s): 0  Gene Names: bamC Membrane Entity: Yes
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12)) Explore P0A903  Go to UniProtKB:  P0A903

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamD	D	226	Escherichia coli	Mutation(s): 0  Gene Names: bamD Membrane Entity: Yes
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12)) Explore P0AC02  Go to UniProtKB:  P0AC02

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamE	E	104	Escherichia coli	Mutation(s): 0  Gene Names: smpA, bamE, SAMEA3752557_04545 Membrane Entity: Yes
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12)) Explore P0A937  Go to UniProtKB:  P0A937

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1-4487
MODEL REFINEMENT	ISOLDE	1.4

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Machin, J.M., Radford, S.E., Ranson, N.A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	222373/Z/21/Z

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Database references
• Version 1.2: 2023-09-06
  Changes: Database references