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Yorodumi- EMDB-21362: Negative stain map of TriABC triclosan efflux pump from Pseudomon... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21362 | |||||||||||||||||||||
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Title | Negative stain map of TriABC triclosan efflux pump from Pseudomonas aeruginosa | |||||||||||||||||||||
Map data | Negative staining map of the TriABC triclosan efflux pump from Pseudomonas aeruginosa, C3 imposed | |||||||||||||||||||||
Sample |
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Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||||||||||||||
Authors | Rouiller I / Fabre L / Sygusch J | |||||||||||||||||||||
Funding support | Canada, United States, Australia, 6 items
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Citation | Journal: Structure / Year: 2021 Title: A "Drug Sweeping" State of the TriABC Triclosan Efflux Pump from Pseudomonas aeruginosa. Authors: Lucien Fabre / Abigail T Ntreh / Amira Yazidi / Inga V Leus / Jon W Weeks / Sudipta Bhattacharyya / Jakob Ruickoldt / Isabelle Rouiller / Helen I Zgurskaya / Jurgen Sygusch / Abstract: The structure of the TriABC inner membrane component of the triclosan/SDS-specific efflux pump from Pseudomonas aeruginosa was determined by cryoelectron microscopy to 4.5 Å resolution. The ...The structure of the TriABC inner membrane component of the triclosan/SDS-specific efflux pump from Pseudomonas aeruginosa was determined by cryoelectron microscopy to 4.5 Å resolution. The complete structure of the inner membrane transporter TriC of the resistance-nodulation-division (RND) superfamily was solved, including a partial structure of the fused periplasmic membrane fusion subunits, TriA and TriB. The substrate-free conformation of TriABC represents an intermediate step in efflux complex assembly before the engagement of the outer membrane channel. Structural analysis identified a tunnel network whose constriction impedes substrate efflux, indicating inhibition of TriABC in the unengaged state. Blind docking studies revealed binding to TriC at the same loci by substrates and bulkier non-substrates. Together with functional analyses, we propose that selective substrate translocation involves conformational gating at the tunnel narrowing that, together with conformational ordering of TriA and TriB, creates an engaged state capable of mediating substrate efflux. | |||||||||||||||||||||
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_21362.map.gz | 8.1 MB | EMDB map data format | |
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Header (meta data) | emd-21362-v30.xml emd-21362.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_21362.png | 78.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21362 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21362 | HTTPS FTP |
-Validation report
Summary document | emd_21362_validation.pdf.gz | 331.7 KB | Display | EMDB validaton report |
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Full document | emd_21362_full_validation.pdf.gz | 331.3 KB | Display | |
Data in XML | emd_21362_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21362 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21362 | HTTPS FTP |
-Related structure data
Related structure data | 6vejC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10128 (Title: A "drug sweeping" state of the TriABC triclosan efflux pump from Pseudomonas aeruginosa Data size: 238.7 Data #1: Unaligned multi-frame micrographs [micrographs - multiframe] Data #2: Single particles stacks with polished particles [picked particles - multiframe - processed] Data #3: Relion repertory of the final refinement with a symmetry C3 [picked particles - single frame - processed] Data #4: Relion repertory of the final refinement with no symmetry [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21362.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative staining map of the TriABC triclosan efflux pump from Pseudomonas aeruginosa, C3 imposed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5929 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TriAxBC
Entire | Name: TriAxBC |
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Components |
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-Supramolecule #1: TriAxBC
Supramolecule | Name: TriAxBC / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 560 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Details: 100 mM Tris HCl (pH 8.0), 150 mM NaCl, 1 mM PMSF, 0.03% (w/v) DDM |
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Staining | Type: NEGATIVE / Material: Uranyl formate |
Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 11393 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |