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- EMDB-1972: Complex of E. coli MacA-AcrA hybrid and Aa MacA-TolC hybrid dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-1972
TitleComplex of E. coli MacA-AcrA hybrid and Aa MacA-TolC hybrid dimer
Map dataThis is an image of a surface rendered side-view of TolC and AcrA complex
Sample
  • Sample: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer
  • Protein or peptide: MacA-AcrA Hybrid
  • Protein or peptide: Aa MacATolC Hybrid Dimer
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / Resolution: 37.0 Å
AuthorsXu Y / Lee M / Moeller A / Song S / Yoon BY / Kim HM / Jun SY / Lee K / Ha NC
CitationJournal: J Biol Chem / Year: 2011
Title: Funnel-like hexameric assembly of the periplasmic adapter protein in the tripartite multidrug efflux pump in gram-negative bacteria.
Authors: Yongbin Xu / Minho Lee / Arne Moeller / Saemee Song / Bo-Young Yoon / Hong-Man Kim / So-Young Jun / Kangseok Lee / Nam-Chul Ha /
Abstract: Gram-negative bacteria expel diverse toxic chemicals through the tripartite efflux pumps spanning both the inner and outer membranes. The Escherichia coli AcrAB-TolC pump is the principal multidrug ...Gram-negative bacteria expel diverse toxic chemicals through the tripartite efflux pumps spanning both the inner and outer membranes. The Escherichia coli AcrAB-TolC pump is the principal multidrug exporter that confers intrinsic drug tolerance to the bacteria. The inner membrane transporter AcrB requires the outer membrane factor TolC and the periplasmic adapter protein AcrA. However, it remains ambiguous how the three proteins are assembled. In this study, a hexameric model of the adapter protein was generated based on the propensity for trimerization of a dimeric unit, and this model was further validated by presenting its channel-forming property that determines the substrate specificity. Genetic, in vitro complementation, and electron microscopic studies provided evidence for the binding of the hexameric adapter protein to the outer membrane factor in an intermeshing cogwheel manner. Structural analyses suggested that the adapter covers the periplasmic region of the inner membrane transporter. Taken together, we propose an adapter bridging model for the assembly of the tripartite pump, where the adapter protein provides a bridging channel and induces the channel opening of the outer membrane factor in the intermeshing tip-to-tip manner.
History
DepositionSep 30, 2011-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1972.png

Downloads & links

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Map

FileDownload / File: emd_1972.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered side-view of TolC and AcrA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.48 Å/pix.
x 112 pix.
= 613.76 Å		5.48 Å/pix.
x 112 pix.
= 613.76 Å		5.48 Å/pix.
x 112 pix.
= 613.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22 / Movie #1: 0.22
Minimum - Maximum-0.33917034 - 1.33412397
Average (Standard dev.)0.00091516 (±0.04213304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 613.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.485.485.48
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z613.760613.760613.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
D min/max/mean-0.3391.3340.001

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Supplemental data

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Sample components

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Entire : E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer

EntireName: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer
Components
  • Sample: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer
  • Protein or peptide: MacA-AcrA Hybrid
  • Protein or peptide: Aa MacATolC Hybrid Dimer

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Supramolecule #1000: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer

SupramoleculeName: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer / type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: MacA-AcrA Hybrid

MacromoleculeName: MacA-AcrA Hybrid / type: protein_or_peptide / ID: 1 / Name.synonym: AcrA / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: Aa MacATolC Hybrid Dimer

MacromoleculeName: Aa MacATolC Hybrid Dimer / type: protein_or_peptide / ID: 2 / Name.synonym: TolC / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateOct 11, 2010
Image recordingAverage electron dose: 15 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Sample stageSpecimen holder: room temperature / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: whole image
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5 APPION

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