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- PDB-8zar: EmrAB-TolC MFS-type tripartite multidrug efflux pump FA -

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Basic information

Entry
Database: PDB / ID: 8zar
TitleEmrAB-TolC MFS-type tripartite multidrug efflux pump FA
Components
  • Multidrug export protein EmrA
  • Multidrug export protein EmrB
  • Outer membrane protein TolC
KeywordsSTRUCTURAL PROTEIN / Multidrug efflux pump / MFS / EmrAB
Function / homology
Function and homology information


MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / response to steroid hormone ...MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / response to steroid hormone / Antimicrobial resistance / bile acid and bile salt transport / porin activity / Secretion of toxins / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / monoatomic ion channel activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding / plasma membrane
Similarity search - Function
Drug resistance transporter EmrB-like / : / : / EMRA, alpha-helical hairpin domain / AAEA-like beta-barrel domain / Efflux pump membrane protein / : / : / Type I secretion outer membrane protein, TolC / : ...Drug resistance transporter EmrB-like / : / : / EMRA, alpha-helical hairpin domain / AAEA-like beta-barrel domain / Efflux pump membrane protein / : / : / Type I secretion outer membrane protein, TolC / : / Outer membrane efflux protein / Outer membrane efflux protein / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Outer membrane protein TolC / Multidrug export protein EmrB / Multidrug export protein EmrA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsDu, D. / Zhong, Z. / Tuerxunjiang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971133 China
CitationJournal: Nat Commun / Year: 2026
Title: A model for drug transport across two membranes of Gram-negative bacteria by an MFS tripartite assembly.
Authors: Zhaojun Zhong / Tuerxunjiang Maimaiti / Matthew L Jackson / Rui Dong / Xueyan Gao / Qing Ouyang / Wenqian Wang / Jinliang Guo / Shangrong Li / Wenyu Shang / Huajun Liu / Hongnian Jiang / ...Authors: Zhaojun Zhong / Tuerxunjiang Maimaiti / Matthew L Jackson / Rui Dong / Xueyan Gao / Qing Ouyang / Wenqian Wang / Jinliang Guo / Shangrong Li / Wenyu Shang / Huajun Liu / Hongnian Jiang / Shuo Zhang / Ulrich Zachariae / Ben F Luisi / Yanjie Chao / Dijun Du /
Abstract: Transport of proteins and small molecules across cellular membrane is crucial for bacterial interaction with the environment and survival against antibiotics. In Gram-negative bacteria that possess ...Transport of proteins and small molecules across cellular membrane is crucial for bacterial interaction with the environment and survival against antibiotics. In Gram-negative bacteria that possess two layers of membranes, specialized macromolecular machines are required to transport substrates across the cell envelope, often via an indirect stepwise process. The major facilitator superfamily (MFS)-type tripartite efflux pumps use proton electrochemical gradient to extrude drugs in diverse bacterial species, but the architecture of the assembly and structural mechanisms remain elusive. A representative MFS-type tripartite efflux pump, EmrAB-TolC, mediates resistance to multiple antimicrobial drugs through proton-coupled EmrB, a member of the DHA2 transporter family. Here, we report the high-resolution (3.13 Å) structure of the EmrAB-TolC pump, revealing a distinct, asymmetric architecture emerging from the assembly of TolC:EmrA:EmrB with a ratio of 3:6:1 and contacts that are essential for the pump assembly. Key residues involved in drug transport are identified and corroborated by mutagenesis and antibiotic sensitivity assays. The structural and functional data support a model for one-step drug transport by the MFS pump across the entire envelope of Gram-negative bacteria.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug export protein EmrA
B: Multidrug export protein EmrA
C: Multidrug export protein EmrA
D: Multidrug export protein EmrA
E: Multidrug export protein EmrA
F: Multidrug export protein EmrA
J: Multidrug export protein EmrB
G: Outer membrane protein TolC
H: Outer membrane protein TolC
I: Outer membrane protein TolC


Theoretical massNumber of molelcules
Total (without water)495,58710
Polymers495,58710
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Multidrug export protein EmrA


Mass: 43977.988 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: emrA / Production host: Escherichia coli B (bacteria) / References: UniProt: P27303
#2: Protein Multidrug export protein EmrB


Mass: 67336.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: emrB / Production host: Escherichia coli B (bacteria) / References: UniProt: P0AEJ0
#3: Protein Outer membrane protein TolC / Multidrug efflux pump subunit TolC / Outer membrane factor TolC


Mass: 54794.344 Da / Num. of mol.: 3 / Mutation: V191L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: tolC / Production host: Escherichia coli B (bacteria) / References: UniProt: P02930
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: EmrABTolC / Type: COMPLEX / Entity ID: #1, #3, #2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 56.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18440 / Symmetry type: POINT

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