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- EMDB-21361: TriABC triclosan efflux pump from Pseudomonas aeruginosa- No symmetry -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21361 | |||||||||||||||||||||
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Title | TriABC triclosan efflux pump from Pseudomonas aeruginosa- No symmetry | |||||||||||||||||||||
![]() | CryoEM map of the TriABC triclosan efflux pump from Pseudomonas aeruginosa,no symmetry imposed | |||||||||||||||||||||
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Biological species | ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||||||||||||||
![]() | Rouiller I / Fabre L / Bhattacharyya S / Sygusch J | |||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 135.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vejC C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() 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]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of the TriABC triclosan efflux pump from Pseudomonas aeruginosa,no symmetry imposed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5531 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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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: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Experimental: 560 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 3483 / Average electron dose: 50.0 e/Å2 Details: 1084 images were kept for single particle analysis after exclusion of images that had no graphene oxide and proteins. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Details | Subunits A-C were modeled with I-TASSER using CusA (3NE5) and then fitted into the EM density and refined with Phenix. Model was rebuilt using Coot. The N-terminal regions of subunits P-R were modeled with I-TASSER based on MP domain of 3LNN while C-terminal regions of subunits P-R were modelled based on MP domain of 2V4D and similarly refined with model rebuilding. | ||||||||
Refinement | Space: REAL / Protocol: AB INITIO MODEL |