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Yorodumi- PDB-5v5s: multi-drug efflux; membrane transport; RND superfamily; Drug resi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v5s | ||||||
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Title | multi-drug efflux; membrane transport; RND superfamily; Drug resistance | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / multi-drug efflux / membrane transport / RND superfamily / Drug resistance | ||||||
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 / xenobiotic transport / bile acid and bile salt transport / porin 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 / xenobiotic transport / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / 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 / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||
Authors | wang, Z. / fan, G. / Hryc, C.F. / Blaza, J.N. / Serysheva, I.I. / Schmid, M.F. / Chiu, W. / Luisi, B.F. / Du, D. | ||||||
Citation | Journal: Elife / Year: 2017 Title: An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump. Authors: Zhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du / Abstract: Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell ...Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump. | ||||||
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 | 5v5s.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5v5s.ent.gz | 984.5 KB | Display | PDB format |
PDBx/mmJSON format | 5v5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v5s_validation.pdf.gz | 789.2 KB | Display | wwPDB validaton report |
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Full document | 5v5s_full_validation.pdf.gz | 968.7 KB | Display | |
Data in XML | 5v5s_validation.xml.gz | 186.3 KB | Display | |
Data in CIF | 5v5s_validation.cif.gz | 277.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/5v5s ftp://data.pdbj.org/pub/pdb/validation_reports/v5/5v5s | HTTPS FTP |
-Related structure data
Related structure data | 8636MC 3636C 8640C 5nc5C 5ng5C 5o66C 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: 48673.801 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503 Production host: Escherichia coli (E. coli) / References: UniProt: P02930 #2: Protein | Mass: 42253.551 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrA, Z0578, ECs0516 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE07, UniProt: P0AE06*PLUS #3: Protein | Mass: 113681.242 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224 |
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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: AcrABTolC in apo state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: AcrABTolC complex in apo state |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 20 K Details: a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh) |
-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: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 45 |
-Processing
Software | Name: PHENIX / Version: dev_2415: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 95410 / Details: auto box by relion | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13544 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Due to the weaker resolution, stronger stereochemical ...Details: Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Due to the weaker resolution, stronger stereochemical and secondary structure restraints were used to ensure that alpha-helices and beta-sheets did not deviate far from their expected geometry. Manual adjustments were kept to a minimum to reduce human bias in the modeling procedure, with Coot only being used to fix obvious errors such as C-beta deviations. A final check of MolProbity and cross correlation was done to ensure model quality. | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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