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- EMDB-24609: Subnanometer in situ structure of the AcrAB-TolC efflux pump boun... -

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Entry
Database: EMDB / ID: EMD-24609
TitleSubnanometer in situ structure of the AcrAB-TolC efflux pump bound with MBX
Map dataSubnanometer in situ structure of the AcrAB-TolC efflux pump bound with MBX
Sample
  • Complex: AcrAB-TolC
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 7.0 Å
AuthorsMuyuan MC / Zhao ZW
Funding support United States, 7 items
OrganizationGrant numberCountry
Welch FoundationQ-1967-20180324 United States
Welch FoundationAU-2014-2019330 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM072804 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM121203 United States
European Research Council (ERC)742210 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143380 United States
CitationJournal: Structure / Year: 2022
Title: In situ structure of the AcrAB-TolC efflux pump at subnanometer resolution.
Authors: Muyuan Chen / Xiaodong Shi / Zhili Yu / Guizhen Fan / Irina I Serysheva / Matthew L Baker / Ben F Luisi / Steven J Ludtke / Zhao Wang /
Abstract: The tripartite AcrAB-TolC assembly, which spans both the inner and outer membranes in Gram-negative bacteria, is an efflux pump that contributes to multidrug resistance. Here, we present the in situ ...The tripartite AcrAB-TolC assembly, which spans both the inner and outer membranes in Gram-negative bacteria, is an efflux pump that contributes to multidrug resistance. Here, we present the in situ structure of full-length Escherichia coli AcrAB-TolC determined at 7 Å resolution by electron cryo-tomography. The TolC channel penetrates the outer membrane bilayer through to the outer leaflet and exhibits two different configurations that differ by a 60° rotation relative to the AcrB position in the pump assembly. AcrA protomers interact directly with the inner membrane and with AcrB via an interface located in proximity to the AcrB ligand-binding pocket. Our structural analysis suggests that these AcrA-bridged interactions underlie an allosteric mechanism for transmitting drug-evoked signals from AcrB to the TolC channel within the pump. Our study demonstrates the power of in situ electron cryo-tomography, which permits critical insights into the function of bacterial efflux pumps.
History
DepositionAug 2, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24609.png

Downloads & links

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Map

FileDownload / File: emd_24609.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubnanometer in situ structure of the AcrAB-TolC efflux pump bound with MBX
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 256 pix.
= 427.52 Å		1.67 Å/pix.
x 256 pix.
= 427.52 Å		1.67 Å/pix.
x 256 pix.
= 427.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-15.101165 - 8.2659235
Average (Standard dev.)0.012246055 (±0.14178094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 427.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Subnanometer in situ structure of the AcrAB-TolC efflux...

Fileemd_24609_additional_1.map
AnnotationSubnanometer in situ structure of the AcrAB-TolC efflux pump bound with MBX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Subnanometer in situ structure of the AcrAB-TolC efflux...

Fileemd_24609_additional_2.map
AnnotationSubnanometer in situ structure of the AcrAB-TolC efflux pump bound with MBX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AcrAB-TolC

EntireName: AcrAB-TolC
Components
  • Complex: AcrAB-TolC

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Supramolecule #1: AcrAB-TolC

SupramoleculeName: AcrAB-TolC / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 22345
ExtractionNumber tomograms: 102 / Number images used: 27932
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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