+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12309 | |||||||||
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Title | Trimeric efflux pump Klebsiella TolC in complex with KlebC | |||||||||
Map data | LocScale sharpened map | |||||||||
Sample |
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Keywords | Efflux pump / trimer / complex / MEMBRANE PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Webby MN / Housden NG | |||||||||
Funding support | 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12309.map.gz | 50 MB | EMDB map data format | |
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Header (meta data) | emd-12309-v30.xml emd-12309.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12309_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_12309.png | 39.7 KB | ||
Filedesc metadata | emd-12309.cif.gz | 5.8 KB | ||
Others | emd_12309_additional_1.map.gz emd_12309_additional_2.map.gz emd_12309_additional_3.map.gz | 57.2 MB 80.6 MB 9.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12309 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12309 | HTTPS FTP |
-Validation report
Summary document | emd_12309_validation.pdf.gz | 439 KB | Display | EMDB validaton report |
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Full document | emd_12309_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | emd_12309_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_12309_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12309 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12309 | HTTPS FTP |
-Related structure data
Related structure data | 7ng8MC 7ng9C 7nnaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12309.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | LocScale sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Sharpened map from relion locres job. Requires Zflip
File | emd_12309_additional_1.map | ||||||||||||
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Annotation | Sharpened map from relion locres job. Requires Zflip | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map from relion refine3D job. Requires zflip
File | emd_12309_additional_2.map | ||||||||||||
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Annotation | Unsharpened map from relion refine3D job. Requires zflip | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Postprocess masked map from relion. Requires Zflip
File | emd_12309_additional_3.map | ||||||||||||
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Annotation | Postprocess masked map from relion. Requires Zflip | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homotrimer of TolC from klebsiella in complex with KlebC
Entire | Name: Homotrimer of TolC from klebsiella in complex with KlebC |
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Components |
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-Supramolecule #1: Homotrimer of TolC from klebsiella in complex with KlebC
Supramolecule | Name: Homotrimer of TolC from klebsiella in complex with KlebC type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Klebsiella quasipneumoniae (bacteria) |
-Macromolecule #1: Outer membrane channel protein
Macromolecule | Name: Outer membrane channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella quasipneumoniae (bacteria) |
Molecular weight | Theoretical: 54.058676 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKKLLPILIG LSLTGFSAMS QAENLLQVYQ QARISNPDLR KSAADRDAAF EKINEARSPL LPQLGLGADY TYTSGFRDYK DQNSNVTSG SLQLTQVLFD MSKWRALTLQ EKAAGIQDVT YQTDQQTLIL NTATAYFKVL AAIDTLSYTE AQKQAIYRQL D QTTQRFNV ...String: MKKLLPILIG LSLTGFSAMS QAENLLQVYQ QARISNPDLR KSAADRDAAF EKINEARSPL LPQLGLGADY TYTSGFRDYK DQNSNVTSG SLQLTQVLFD MSKWRALTLQ EKAAGIQDVT YQTDQQTLIL NTATAYFKVL AAIDTLSYTE AQKQAIYRQL D QTTQRFNV GLVAITDVQN ARSQYDAVLA NEVTARNDLD NAVEELRQVT GNYYPELASL NVDGFKTSKP QAVNALLKEA EN RNLSLLQ ARLNQDLARE QIRQAQDGHL PTLDLNASSG VSNNRYSGSK SISQDADIGQ NKIGLSFSLP LYQGGMVNSQ VKQ AQYNFV GASEQLESAH RSVVQTVRSS FNNVNASISS INAYKQAVVS AQSSLDAMEA GYSVGTRTIV DVLDATTTLY NAKQ QLSNA RYNYLINELN IKSALGTLNE QDLIALNNTL GKPISTSADS VAPENPQQDA TADGYGNTTA AMKPASARTT THSSG SNPF RQLEHHHHHH UniProtKB: Outer membrane channel protein TolC |
-Macromolecule #2: Klebicin C activity
Macromolecule | Name: Klebicin C activity / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella quasipneumoniae (bacteria) |
Molecular weight | Theoretical: 28.629162 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MADNQPVPLT PAPPGMVSLG VNENGEEEMT VIGGDGSGTG FSGNEAPIIP GSGSLQADLG KKSLTRLQAE SSAAIHATAK WTTENLAKT QAAQAERAKA AMLSQQAAKA KQAKLTQHLK DVVDRALQNN KTRPTVIDLA HQNNQQMAAM AEFIGRQKAI E EARKKAER ...String: MADNQPVPLT PAPPGMVSLG VNENGEEEMT VIGGDGSGTG FSGNEAPIIP GSGSLQADLG KKSLTRLQAE SSAAIHATAK WTTENLAKT QAAQAERAKA AMLSQQAAKA KQAKLTQHLK DVVDRALQNN KTRPTVIDLA HQNNQQMAAM AEFIGRQKAI E EARKKAER EAKRAEEAYQ AALRAQEEEQ RKQAEIERKL QEARKQEAAA KAKAEADRIA AEKAEAEARA KAEAERRKAE EA RKALFAK AGIKDTPGCL EHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.9 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |