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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 data
SampleE. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer:
MacA-AcrA Hybrid / Aa MacATolC Hybrid Dimer
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / Resolution: 37 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.
Validation ReportSummary, Full report, XML, About validation report
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

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)
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
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 / Number of components: 2

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Component #1: protein, MacA-AcrA Hybrid

ProteinName: MacA-AcrA Hybrid / a.k.a: AcrA / Oligomeric Details: hexamer / Recombinant expression: Yes
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Aa MacATolC Hybrid Dimer

ProteinName: Aa MacATolC Hybrid Dimer / a.k.a: TolC / Oligomeric Details: hexamer / Recombinant expression: Yes
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Oct 11, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm
Specimen HolderHolder: room temperature / Model: SIDE ENTRY, EUCENTRIC

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: projection matching / Software: IMAGIC-5 APPION / CTF correction: whole image / Resolution: 37 Å / Resolution method: FSC 0.5

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