+Open data
-Basic information
Entry | Database: PDB / ID: 8bwc | ||||||
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Title | E. coli BAM complex (BamABCDE) wild-type | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Outer Membrane Protein / Protein Folding / beta barrel | ||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Escherichia coli BL21 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Machin, J.M. / Radford, S.E. / Ranson, N.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Angew Chem Int Ed Engl / Year: 2023 Title: Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. Authors: Samuel F Haysom / Jonathan Machin / James M Whitehouse / Jim E Horne / Katherine Fenn / Yue Ma / Hassane El Mkami / Nils Böhringer / Till F Schäberle / Neil A Ranson / Sheena E Radford / Christos Pliotas / 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 ...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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bwc.cif.gz | 481.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bwc.ent.gz | 387.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bwc_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8bwc_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8bwc_validation.xml.gz | 55.4 KB | Display | |
Data in CIF | 8bwc_validation.cif.gz | 81.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/8bwc ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwc | HTTPS FTP |
-Related structure data
Related structure data | 16282MC 8bvqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 88514.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: 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_ ...Gene: 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 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TPJ2 |
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#2: Protein | Mass: 39882.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: bamB, yfgL, b2512, JW2496 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P77774 |
#3: Protein | Mass: 34401.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3T0D3 |
#4: Protein | Mass: 25816.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3SYV7 |
#5: Protein | Mass: 11610.833 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: smpA, bamE, SAMEA3752557_04545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X7FA24 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.20098298 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.58 sec. / Electron dose: 44.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6063 |
EM imaging optics | Energyfilter name: TFS Selectris / Energyfilter slit width: 10 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 656080 | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169599 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | B value: 82 / Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.29 Å2 | |||||||||||||||||||||||||||||||||||
Refine LS restraints |
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