+Open data
-Basic information
Entry | Database: PDB / ID: 6v05 | |||||||||||||||
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Title | Cryo-EM structure of a substrate-engaged Bam complex | |||||||||||||||
Components | (Outer membrane protein assembly factor ...) x 6 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / beta-barrel / insertase | |||||||||||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / identical protein binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) Escherichia coli K-12 (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
Authors | Tomasek, D. / Rawson, S. / Lee, J. / Wzorek, J.S. / Harrison, S.C. / Li, Z. / Kahne, D. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nature / Year: 2020 Title: Structure of a nascent membrane protein as it folds on the BAM complex. Authors: David Tomasek / Shaun Rawson / James Lee / Joseph S Wzorek / Stephen C Harrison / Zongli Li / Daniel Kahne / Abstract: Mitochondria, chloroplasts and Gram-negative bacteria are encased in a double layer of membranes. The outer membrane contains proteins with a β-barrel structure. β-Barrels are sheets of β-strands ...Mitochondria, chloroplasts and Gram-negative bacteria are encased in a double layer of membranes. The outer membrane contains proteins with a β-barrel structure. β-Barrels are sheets of β-strands wrapped into a cylinder, in which the first strand is hydrogen-bonded to the final strand. Conserved multi-subunit molecular machines fold and insert these proteins into the outer membrane. One subunit of the machines is itself a β-barrel protein that has a central role in folding other β-barrels. In Gram-negative bacteria, the β-barrel assembly machine (BAM) consists of the β-barrel protein BamA, and four lipoproteins. To understand how the BAM complex accelerates folding without using exogenous energy (for example, ATP), we trapped folding intermediates on this machine. Here we report the structure of the BAM complex of Escherichia coli folding BamA itself. The BamA catalyst forms an asymmetric hybrid β-barrel with the BamA substrate. The N-terminal edge of the BamA catalyst has an antiparallel hydrogen-bonded interface with the C-terminal edge of the BamA substrate, consistent with previous crosslinking studies; the other edges of the BamA catalyst and substrate are close to each other, but curl inward and do not pair. Six hydrogen bonds in a membrane environment make the interface between the two proteins very stable. This stability allows folding, but creates a high kinetic barrier to substrate release after folding has finished. Features at each end of the substrate overcome this barrier and promote release by stepwise exchange of hydrogen bonds. This mechanism of substrate-assisted product release explains how the BAM complex can stably associate with the substrate during folding and then turn over rapidly when folding is complete. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v05.cif.gz | 335 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v05.ent.gz | 264.2 KB | Display | PDB format |
PDBx/mmJSON format | 6v05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v05_validation.pdf.gz | 718.2 KB | Display | wwPDB validaton report |
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Full document | 6v05_full_validation.pdf.gz | 738 KB | Display | |
Data in XML | 6v05_validation.xml.gz | 53.8 KB | Display | |
Data in CIF | 6v05_validation.cif.gz | 80.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/6v05 ftp://data.pdbj.org/pub/pdb/validation_reports/v0/6v05 | HTTPS FTP |
-Related structure data
Related structure data | 20969MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Outer membrane protein assembly factor ... , 6 types, 6 molecules ABCDEF
#1: Protein | Mass: 90567.227 Da / Num. of mol.: 1 / Mutation: C690S, C700S, F804C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A940 |
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#2: Protein | Mass: 41918.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P77774 |
#3: Protein | Mass: 36875.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 Gene: bamC, nlpB, A6581_02455, A6592_19755, A8C65_04235, A8G17_10975, AC067_02730, AC789_1c28090, ACN002_2512, ACN68_11560, ACN81_26800, ACU57_04515, ACU90_01100, AKG99_13055, AM270_06735, AM446_ ...Gene: bamC, nlpB, A6581_02455, A6592_19755, A8C65_04235, A8G17_10975, AC067_02730, AC789_1c28090, ACN002_2512, ACN68_11560, ACN81_26800, ACU57_04515, ACU90_01100, AKG99_13055, AM270_06735, AM446_08445, AM464_03885, AML07_10810, AML35_21815, APT94_12605, APZ14_05885, AUQ13_12835, AUS26_08895, AW106_01925, AWP75_05795, B1K96_18050, B9M99_18180, B9T59_21405, BANRA_01021, BANRA_03170, BANRA_04601, BB545_17690, BE963_28130, BEN53_15545, BER14_02350, BHF46_00865, BHS81_15170, BIQ87_14450, BIU72_15910, BIZ41_13405, BK248_16985, BK292_09100, BK373_06140, BK375_00595, BK383_22560, BK400_08740, BMT91_12040, BOH76_02570, BON66_22990, BON69_13590, BON71_05810, BON75_17940, BON76_02345, BON81_08015, BON83_11105, BON86_12870, BON92_23095, BON94_05640, BON95_12010, BON96_16290, BTQ06_24710, BUE81_00175, BvCms2454_00576, BvCms28BK_03651, BvCmsA75A_03498, BvCmsC61A_03920, BvCmsHHP001_02989, BvCmsHHP019_02257, BvCmsHHP056_03727, BvCmsKKP061_00365, BvCmsKSNP019_02678, BvCmsKSNP073_01370, BvCmsKSNP081_01804, BvCmsKSNP120_01449, BvCmsKSP011_03652, BvCmsKSP024_03770, BvCmsKSP026_00127, BvCmsKSP045_01057, BvCmsKSP058_05104, BvCmsKSP067_01143, BvCmsNSNP036_03233, BvCmsNSP007_05045, BvCmsNSP047_01191, BvCmsNSP072_03470, BvCmsSINP011_00589, BvCmsSINP012_02461, BvCmsSINP022_03246, BVL39_14450, BW690_08400, BXT93_09065, BZL31_19830, BZL69_23975, C3449_00575, C4J69_10905, C5N07_10515, C5P01_06205, C5P43_23745, C5P44_22155, C6669_16365, C6986_16055, C7235_07205, C9025_02075, C9083_01895, C9212_02290, C9299_09010, C9E25_13305, C9Y80_06105, C9Y95_21475, C9Z12_16640, CA593_14465, CDL37_24220, CEG98_13220, CG692_24660, CI641_005275, CI694_19990, CIJ94_07570, COD30_00650, COD46_27330, CQP61_08535, CR538_07295, CRM83_27895, CRT46_14950, CWM24_12580, CWS33_10415, CY655_15855, D2184_13985, D2188_18170, D3821_11830, D3822_05395, D3O91_03970, D3Y67_12985, D9D31_00585, D9D43_09275, D9E34_00585, D9E35_17030, D9F17_05285, D9G42_10275, D9G48_19890, D9H68_00610, D9H70_20745, D9H94_18900, D9I11_00510, D9I18_08285, D9I87_03080, D9I88_00655, D9J11_04670, D9J44_00445, D9J60_12530, D9K48_26220, D9K54_08830, DAH27_02200, DAH30_02900, DAH34_02675, DAH37_19960, DBQ99_07990, DD762_13530, DEN86_22815, DEN89_10395, DEN97_02085, DEO19_00630, DIV22_31745, DL545_07645, DL800_18795, DM102_07120, DM129_09435, DNQ41_17525, DNQ45_02690, DP258_07610, DQE83_18935, DQF57_11025, DQO13_11190, DS732_18480, DTL43_01510, DTL90_08635, DTM10_01015, DTM25_19255, DTM45_09650, DU321_10720, DWB25_07365, DXT71_21935, E2112_00485, E2115_16230, E2119_05135, E2126_07380, E2127_04515, E2129_06730, E2132_10070, E2134_09470, E2135_00555, E2855_03225, E2863_03132, E5S46_08270, E5S47_00585, E5S58_10625, E5S61_11100, EAI42_12280, EAI52_02570, EC1094V2_1211, EC3234A_44c00830, EC382_03360, EC95NR1_01696, ECTO6_01409, ED600_00620, ED648_19505, EEP23_23015, EHH55_03705, EIA21_06830, EJC75_11395, EKI52_22355, EL75_1174, EL79_1185, EL80_1190, ELT58_05595, ELU85_09985, ELV08_03665, ELV26_03145, ELV28_11920, EO240_05615, EO241_29005, EPS71_00265, EPS97_10555, EPT01_15160, EQ820_10645, EQ823_08955, EQ825_24025, EQ830_05480, ERL57_11390, ERS085365_02853, ERS085366_00345, ERS085374_00117, ERS085379_00986, ERS085383_02107, ERS085386_00039, ERS085404_01131, ERS085416_01322, ERS139211_02639, ERS150876_00778, ExPECSC038_04470, EXX06_10435, EXX13_08605, EXX23_06350, EXX40_08105, EXX53_08115, EXX55_10135, EXX71_05165, EXX73_17945, EXX78_07240, EXX87_17745, EYD11_06585, EYY78_21115, FAX15_16530, FE198_07360, FNJ69_10855, FNJ79_09165, FNJ83_16390, FORC28_1482, FQR64_06705, FV293_04230, HmCms184_03495, HmCmsJML072_03247, HmCmsJML074_00064, HmCmsJML204_03962, HMPREF3040_02807, HW43_16770, JD73_18025, MJ49_18500, NCTC10090_04434, NCTC10764_00647, NCTC10865_01743, NCTC11022_02534, NCTC11126_06126, NCTC11181_03634, NCTC11341_00816, NCTC12950_01648, NCTC13148_02274, NCTC13462_05111, NCTC13846_01494, NCTC7927_01568, NCTC8621_01448, NCTC8960_04114, NCTC9036_01478, NCTC9044_00198, NCTC9045_01669, NCTC9050_04702, NCTC9055_03350, NCTC9062_01737, NCTC9077_01815, NCTC9111_01883, NCTC9117_01960, NCTC9119_01583, NCTC9702_01656, NCTC9703_01031, NCTC9706_04674, NCTC9969_01610, PGD_00767, RG28_09510, RK56_024525, RX35_01364, SAMEA3472033_00601, SAMEA3472043_00977, SAMEA3472044_02057, SAMEA3472047_03903, SAMEA3472055_00995, SAMEA3472056_00816, SAMEA3472070_00123, SAMEA3472080_01551, SAMEA3472090_01290, SAMEA3472108_03434, SAMEA3472147_00102, SAMEA3484427_00337, SAMEA3484429_00446, SAMEA3484434_00350, SAMEA3485101_04932, SAMEA3485113_01786, SAMEA3752557_01026, SAMEA3752559_00799, SAMEA3752620_00108, SAMEA3753097_02061, SAMEA3753164_00674, SAMEA3753300_00970, SK85_02726, UC41_17115, UN86_00295, UN91_14105, WQ89_05460, WR15_19465, YDC107_1000 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8SZY2, UniProt: P0A903*PLUS |
#4: Protein | Mass: 27858.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: yfiO, bamD, ECIAI39_2800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3MJ38, UniProt: P0AC02*PLUS |
#5: Protein | Mass: 13530.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: smpA, bamE, NCTC8196_03449 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3S5E0E0, UniProt: P0A937*PLUS |
#6: Protein | Mass: 64010.285 Da / Num. of mol.: 1 Mutation: T467C,C690S,C700S,deletion of residues 172-421,deletion of residues 430-439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A940 |
-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 | Name: BamABCDE bound to substrate BamA with loop 1 deleted / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli K-12 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 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: OTHER |
Electron lens | Mode: OTHER / Calibrated magnification: 58717 X / Calibrated defocus min: 1100 nm / Calibrated defocus max: 2800 nm |
Image recording | Average exposure time: 3 sec. / Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 4097 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 2054956 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223353 / Symmetry type: POINT |