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- EMDB-44385: The in situ structure of MacAB-TolC in erythromycin-present state -

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Basic information

Entry
Database: EMDB / ID: EMD-44385
TitleThe in situ structure of MacAB-TolC in erythromycin-present state
Map data
Sample
  • Cell: MacAB-TolC expressing E. coli
Keywordstripartite efflux pump / MacAB-TolC / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsHuo T / Yu Z / Wang Z
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143380 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL162842 United States
Welch FoundationQ-2173-20230405 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190602 United States
CitationJournal: Commun Biol / Year: 2025
Title: In situ structure and assembly of the ABC-type tripartite pump MacAB-TolC.
Authors: Tong Huo / Wenfang Zhang / Zhili Yu / Wei Zheng / Yaoming Wu / Qiuyu Ren / Zekai Wan / Junli Cao / Zhao Wang / Xiaodong Shi /
Abstract: The MacAB-TolC tripartite efflux pump is widely distributed in Gram-negative bacteria, extruding antibiotics and virulence factors that lead to multidrug resistance and pathogenicity. However, the in ...The MacAB-TolC tripartite efflux pump is widely distributed in Gram-negative bacteria, extruding antibiotics and virulence factors that lead to multidrug resistance and pathogenicity. However, the in situ structure and assembly mechanism of MacAB-TolC remain unclear. Here, we resolve the in situ structures of the MacAB-TolC efflux pump in Escherichia coli by electron cryo-tomography and subtomogram averaging. In the cells without antibiotic treatment, we observe a fully assembled MacAB-TolC pump. When Escherichia coli cells are treated with erythromycin, in addition to the tripartite pumps, we also discover the emergence of MacA-TolC subcomplexes without MacB, indicating flexible binding of MacB in the presence of an antibiotic substrate, which is further validated by in vivo photo-crosslinking results. Together, our data suggest the in situ assembly process of MacAB-TolC starts from the formation of MacA-TolC subcomplex, and provides insights into the design of efflux pump inhibitors.
History
DepositionApr 2, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44385.png

Downloads & links

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Map

FileDownload / File: emd_44385.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 240 pix.
= 422.4 Å		1.76 Å/pix.
x 240 pix.
= 422.4 Å		1.76 Å/pix.
x 240 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.64
Minimum - Maximum-15.378978999999999 - 23.634679999999999
Average (Standard dev.)0.016018363 (±0.99312675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44385_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44385_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MacAB-TolC expressing E. coli

EntireName: MacAB-TolC expressing E. coli
Components
  • Cell: MacAB-TolC expressing E. coli

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Supramolecule #1: MacAB-TolC expressing E. coli

SupramoleculeName: MacAB-TolC expressing E. coli / type: cell / 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: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
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: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1438
ExtractionNumber tomograms: 68 / Number images used: 2094
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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