+Open data
-Basic information
Entry | Database: PDB / ID: 7ng8 | ||||||
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Title | Trimeric efflux pump Klebsiella TolC in complex with KlebC | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Efflux pump / trimer / complex | ||||||
Function / homology | Type I secretion outer membrane protein, TolC / : / Outer membrane efflux protein / Outer membrane efflux protein / efflux transmembrane transporter activity / cell outer membrane / Outer membrane channel protein TolC Function and homology information | ||||||
Biological species | Klebsiella quasipneumoniae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Webby, M.N. / Housden, N.G. / Kleanthous, C. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Toxin import through the antibiotic efflux channel TolC. Authors: Nicholas G Housden / Melissa N Webby / Edward D Lowe / Tarick J El-Baba / Renata Kaminska / Christina Redfield / Carol V Robinson / Colin Kleanthous / Abstract: Bacteria often secrete diffusible protein toxins (bacteriocins) to kill bystander cells during interbacterial competition. Here, we use biochemical, biophysical and structural analyses to show how a ...Bacteria often secrete diffusible protein toxins (bacteriocins) to kill bystander cells during interbacterial competition. Here, we use biochemical, biophysical and structural analyses to show how a bacteriocin exploits TolC, a major outer-membrane antibiotic efflux channel in Gram-negative bacteria, to transport itself across the outer membrane of target cells. Klebicin C (KlebC), a rRNase toxin produced by Klebsiella pneumoniae, binds TolC of a related species (K. quasipneumoniae) with high affinity through an N-terminal, elongated helical hairpin domain common amongst bacteriocins. The KlebC helical hairpin opens like a switchblade to bind TolC. A cryo-EM structure of this partially translocated state, at 3.1 Å resolution, reveals that KlebC associates along the length of the TolC channel. Thereafter, the unstructured N-terminus of KlebC protrudes beyond the TolC iris, presenting a TonB-box sequence to the periplasm. Association with proton-motive force-linked TonB in the inner membrane drives toxin import through the channel. Finally, we demonstrate that KlebC binding to TolC blocks drug efflux from bacteria. Our results indicate that TolC, in addition to its known role in antibiotic export, can function as a protein import channel for bacteriocins. | ||||||
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 | 7ng8.cif.gz | 431.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ng8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ng8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ng8_validation.pdf.gz | 779.7 KB | Display | wwPDB validaton report |
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Full document | 7ng8_full_validation.pdf.gz | 789.4 KB | Display | |
Data in XML | 7ng8_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 7ng8_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/7ng8 ftp://data.pdbj.org/pub/pdb/validation_reports/ng/7ng8 | HTTPS FTP |
-Related structure data
Related structure data | 12309MC 7ng9C 7nnaC 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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-Components
#1: Protein | Mass: 54058.676 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella quasipneumoniae (bacteria) Gene: tolC, CP911_05930, DBL00_17640, G5630_14450, SAMEA104168726_00630, SAMEA3531848_02756 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C3Q001 #2: Protein | | Mass: 28629.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella quasipneumoniae (bacteria) / Gene: kca / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-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: Homotrimer of TolC from klebsiella in complex with KlebC Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Klebsiella quasipneumoniae (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 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 |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435603 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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