- EMDB-21960: Colicin E1 fragment in nanodisc-embedded TolC -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-21960
Title
Colicin E1 fragment in nanodisc-embedded TolC
Map data
C3-symmetrized map of nanodisc-embedded TolC
Sample
Complex: Outer membrane protein TolC
Protein or peptide: Outer membrane protein TolC
Keywords
antibiotic efflux / bacteriocin / TRANSPORT PROTEIN
Function / homology
Function and homology information
MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity ...MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity / monoatomic ion transmembrane transport / cell outer membrane / response to organic cyclic compound / response to toxic substance / monoatomic ion channel activity / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane Similarity search - Function
: / Type I secretion outer membrane protein, TolC / Outer membrane efflux protein / Outer membrane efflux protein Similarity search - Domain/homology
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
DP2GM128201
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P20GM113117
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P20GM103638
United States
Citation
Journal: Elife / Year: 2022 Title: Colicin E1 opens its hinge to plug TolC. Authors: S Jimmy Budiardjo / Jacqueline J Stevens / Anna L Calkins / Ayotunde P Ikujuni / Virangika K Wimalasena / Emre Firlar / David A Case / Julie S Biteen / Jason T Kaelber / Joanna S G Slusky / Abstract: The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed ...The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, that hijacks the outer membrane proteins (OMPs) TolC and BtuB to enter the cell. Here, we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryo-electron microscopy to obtain the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore-an architectural rearrangement from colicin E1's unbound conformation. This binding is stable in live cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plug the channel, inhibiting its native efflux function as an antibiotic efflux pump, and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other OMP functions.
History
Deposition
May 10, 2020
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Header (metadata) release
May 12, 2021
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Map release
May 12, 2021
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Update
May 15, 2024
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Current status
May 15, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Model: UltrAuFoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TALOS ARCTICA
Specialist optics
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 16443 / Average exposure time: 8.0 sec. / Average electron dose: 33.04 e/Å2 / Details: 5 frames per second
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
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