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- PDB-9lyq: Structure of RND efflux pump MdtB -

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Basic information

Entry
Database: PDB / ID: 9lyq
TitleStructure of RND efflux pump MdtB
ComponentsMultidrug resistance protein MdtB
KeywordsTRANSPORT PROTEIN / Membrane protein / E.coli. / Cryo-EM / Efflux pump.
Function / homologyMultidrug resistance protein MdtB / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / xenobiotic transmembrane transporter activity / plasma membrane / Multidrug resistance protein MdtB
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsDutta, S. / Padmanaban, S. / Fernando, R.C.
Funding support India, 3items
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
DepositionFeb 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Multidrug resistance protein MdtB
C: Multidrug resistance protein MdtB
D: Multidrug resistance protein MdtB


Theoretical massNumber of molelcules
Total (without water)336,4613
Polymers336,4613
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Multidrug resistance protein MdtB / Multidrug transporter MdtB / RND efflux pump MdtB


Mass: 112153.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mdtB, BWG_1865 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C4ZSG3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotrimeric form of RND efflux pump, MdtB / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252085 / Symmetry type: POINT

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