8BWC

E. coli BAM complex (BamABCDE) wild-type

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA790Escherichia coliMutation(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

UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A940
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamB373Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: bamB, yfgL, b2512, JW2496
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
Go to UniProtKB:  P77774
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamC320Escherichia coliMutation(s): 0 
Gene Names: bamC
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A903
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamD226Escherichia coliMutation(s): 0 
Gene Names: bamD
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC02
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamE104Escherichia coliMutation(s): 0 
Gene Names: smpA, bamE, SAMEA3752557_04545
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A937
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTISOLDE1.4

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom222373/Z/21/Z

Revision History  (Full details and data files)

  • 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