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- EMDB-63315: The asymmetric structure of MdtF from E.coli. -

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Basic information

Entry
Database: EMDB / ID: EMD-63315
TitleThe asymmetric structure of MdtF from E.coli.
Map data
Sample
  • Organelle or cellular component: Asymmetric structure of MdtF from E.coli
KeywordsMembrane protein / E.coli. / Cryo-EM / Efflux pump. / TRANSPORT PROTEIN
Function / homology
Function and homology information


xenobiotic transmembrane transport / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / response to toxic substance / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Multidrug resistance protein MdtF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsDutta S / Padmanaban S / Fernando Rencilin C
Funding support India, 3 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
Science and Engineering Research Board (SERB)CRG/2022/002674 India
CitationJournal: mBio / Year: 2026
Title: Cryo-EM reveals the structural heterogeneity and conformational flexibility of multidrug efflux pumps MdtB and MdtF.
Authors: Surekha Padmanaban / Clayton Fernando Rencilin / Rupam Biswas / Somnath Dutta /
Abstract: Resistance-nodulation-cell division (RND) efflux pumps are the major cause of multidrug resistance in bacteria, particularly in Gram-negative bacteria. They are complex molecular machines forming ...Resistance-nodulation-cell division (RND) efflux pumps are the major cause of multidrug resistance in bacteria, particularly in Gram-negative bacteria. They are complex molecular machines forming tripartite assemblies that actively transport out a wide range of antimicrobial agents, including antibiotics, biocides, and host defense molecules. However, the presence of multiple RND transporters with overlapping functions in a single bacterium raises questions about their individual functional relevance. In this study, we determined the cryo-electron microscopy (cryo-EM) structures of two distinct hydrophobic and amphiphilic efflux (HAE)-RND transporters from MdtB and MdtF. MdtB transporter is a part of the two-RND subunit system MdtABC. MdtF is a unique class of RND transporter whose expression is regulated by oxygen availability and is crucial for the survival of in anaerobic growth conditions. The cryo-EM structures of MdtB and MdtF reveal a novel conformational state of HAE-RND efflux pumps. While the MdtB structure adopts an intermediate state, MdtF displays structural dynamics in the presence of n-dodecyl-β-D-maltoside (DDM). MdtF at 2.8 Å resolution displayed a significant conformational change in the transmembrane core helices and flexibility in the transmembrane domain. Our findings highlight the significance of the novel structural state during the substrate transport mechanism. Furthermore, our structural analysis provides insights into drug-binding sites and the transport mechanism of these important transporters.
IMPORTANCE: Resistance-nodulation-cell division (RND) efflux pumps are mainly responsible for multidrug resistance by extruding a wide range of antibiotics from bacterial cells. These pumps are ...IMPORTANCE: Resistance-nodulation-cell division (RND) efflux pumps are mainly responsible for multidrug resistance by extruding a wide range of antibiotics from bacterial cells. These pumps are frequently overexpressed in multidrug-resistant strains, which are responsible for urinary tract infections and foodborne illnesses. In this current study, we resolved the structures of two hydrophobic and amphiphilic efflux (HAE)-RND transporters, MdtB and MdtF, using single-particle cryo-electron microscopy. Our study demonstrated novel structural states of MdtF during substrate transport. This knowledge provides valuable insights into the conformational transitions underlying substrate transport. Understanding these structural mechanisms fills a critical knowledge gap in the RND-mediated efflux process and lays the groundwork for structure-guided inhibitor design. Our findings contribute to ongoing efforts to develop novel therapeutic strategies to combat multidrug-resistant infections.
History
DepositionJan 29, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63315.png

Downloads & links

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Map

FileDownload / File: emd_63315.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.294
Minimum - Maximum-0.5095895 - 1.672555
Average (Standard dev.)-0.0036728834 (±0.056729138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63315_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_63315_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Asymmetric structure of MdtF from E.coli

EntireName: Asymmetric structure of MdtF from E.coli
Components
  • Organelle or cellular component: Asymmetric structure of MdtF from E.coli

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Supramolecule #1: Asymmetric structure of MdtF from E.coli

SupramoleculeName: Asymmetric structure of MdtF from E.coli / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 322240
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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