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- EMDB-10372: CryoEM structure of MexAB-OprM in nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-10372
TitleCryoEM structure of MexAB-OprM in nanodisc
Map data
SampleTripartite complex MexAB-OprM:
mexB / mexA / OprM
Function / homology
Function and homology information


xenobiotic transport / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / response to antibiotic / integral component of membrane / plasma membrane
Hydrophobe/amphiphile efflux-1 HAE1 / Cation efflux system protein CusB, domain 1 / Acriflavin resistance protein / Outer membrane efflux protein / RND efflux pump, membrane fusion protein / RND efflux system, outer membrane lipoprotein, NodT / Membrane lipoprotein, lipid attachment site / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / RND efflux pump, membrane fusion protein, barrel-sandwich domain
Efflux pump membrane transporter / MexA family multidrug efflux RND transporter periplasmic adaptor subunit / Outer membrane protein OprM
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGlavier M / Puvanendran D / Salvador D / Decossas M / Phan G / Garnier C / Frezza E / Cece Q / Schoehn G / Picard M ...Glavier M / Puvanendran D / Salvador D / Decossas M / Phan G / Garnier C / Frezza E / Cece Q / Schoehn G / Picard M / Taveau J-C / Daury L / Broutin I / Lambert O
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR-17CE11-0028 France
CitationJournal: 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.
Validation ReportPDB-ID: 6ta5

SummaryFull reportAbout validation report
History
DepositionOct 9, 2019-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ta5
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10372.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 512 pix.
= 696.32 Å
1.36 Å/pix.
x 512 pix.
= 696.32 Å
1.36 Å/pix.
x 512 pix.
= 696.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.09764242 - 0.17524983
Average (Standard dev.)-0.00000734329 (±0.0052246875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 696.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z696.320696.320696.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0980.175-0.000

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Supplemental data

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Sample components

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Entire Tripartite complex MexAB-OprM

EntireName: Tripartite complex MexAB-OprM / Number of components: 4

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Component #1: protein, Tripartite complex MexAB-OprM

ProteinName: Tripartite complex MexAB-OprM / Recombinant expression: No
SourceSpecies: Pseudomonas aeruginosa (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, mexB

ProteinName: mexB / Recombinant expression: No

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Component #3: protein, mexA

ProteinName: mexA / Recombinant expression: No

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Component #4: protein, OprM

ProteinName: OprM / Recombinant expression: No

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 35819
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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