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Yorodumi- PDB-6ta5: OprM-MexA complex from the MexAB-OprM Pseudomonas aeruginosa whol... -
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-Basic information
Entry | Database: PDB / ID: 6ta5 | ||||||
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Title | OprM-MexA complex from the MexAB-OprM Pseudomonas aeruginosa whole assembly reconstituted in nanodiscs | ||||||
Components |
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Keywords | ANTIMICROBIAL PROTEIN / transporter / efflux / proton motive force / bacterial resistance | ||||||
Function / homology | Function and homology information efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / protein homooligomerization / transmembrane transport / response to antibiotic / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Glavier, M. / Schoehn, G. / Taveau, J.C. / Phan, G. / Daury, L. / Lambert, O. / Broutin, I. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Antibiotic export by MexB multidrug efflux transporter is allosterically controlled by a MexA-OprM chaperone-like complex. Authors: Marie Glavier / Dhenesh Puvanendran / Dimitri Salvador / Marion Decossas / Gilles Phan / Cyril Garnier / Elisa Frezza / Quentin Cece / Guy Schoehn / Martin Picard / Jean-Christophe Taveau / ...Authors: Marie Glavier / Dhenesh Puvanendran / Dimitri Salvador / Marion Decossas / Gilles Phan / Cyril Garnier / Elisa Frezza / Quentin Cece / Guy Schoehn / Martin Picard / Jean-Christophe Taveau / Laetitia Daury / Isabelle Broutin / Olivier Lambert / Abstract: The tripartite multidrug efflux system MexAB-OprM is a major actor in Pseudomonas aeruginosa antibiotic resistance by exporting a large variety of antimicrobial compounds. Crystal structures of MexB ...The tripartite multidrug efflux system MexAB-OprM is a major actor in Pseudomonas aeruginosa antibiotic resistance by exporting a large variety of antimicrobial compounds. Crystal structures of MexB and of its Escherichia coli homolog AcrB had revealed asymmetric trimers depicting a directional drug pathway by a conformational interconversion (from Loose and Tight binding pockets to Open gate (LTO) for drug exit). It remains unclear how MexB acquires its LTO form. Here by performing functional and cryo-EM structural investigations of MexB at various stages of the assembly process, we unveil that MexB inserted in lipid membrane is not set for active transport because it displays an inactive LTC form with a Closed exit gate. In the tripartite complex, OprM and MexA form a corset-like platform that converts MexB into the active form. Our findings shed new light on the resistance nodulation cell division (RND) cognate partners which act as allosteric factors eliciting the functional drug extrusion. | ||||||
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 | 6ta5.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ta5.ent.gz | 883 KB | Display | PDB format |
PDBx/mmJSON format | 6ta5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ta5_validation.pdf.gz | 974.3 KB | Display | wwPDB validaton report |
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Full document | 6ta5_full_validation.pdf.gz | 1015.3 KB | Display | |
Data in XML | 6ta5_validation.xml.gz | 161 KB | Display | |
Data in CIF | 6ta5_validation.cif.gz | 247.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/6ta5 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/6ta5 | HTTPS FTP |
-Related structure data
Related structure data | 10372MC 6t7sC 6ta6C 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: 51737.605 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: trimer of the outer membrane factor OprM / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: oprM, oprK, PA0427 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51487 #2: Protein | Mass: 39462.387 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: trimer of dimers of the membrane fusion protein MexA Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: mexA, CAZ10_35280, CGU42_31245, DT376_09430, DZ934_11470, DZ962_14980, E4V10_16060, EFK68_29775, EQH76_08910, IPC3_09880, IPC669_14605 Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V3GTR8, UniProt: P52477*PLUS #3: Protein | Mass: 113706.008 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: trimer of the RND transporter MexB / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: mexB, mexB_1, C0044_03030, DZ934_11475, E4V10_16065, IPC3_09885, IPC669_14600, PAERUG_E15_London_28_01_14_02845, PAMH19_0483, RW109_RW109_01030 Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q9M6, UniProt: P52002*PLUS |
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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: MexAB-OprM in nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 42 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 364914 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35819 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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