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- EMDB-39879: EmrAB-TolC MFS-type tripartite multidrug efflux pump EA -

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Basic information

Entry
Database: EMDB / ID: EMD-39879
TitleEmrAB-TolC MFS-type tripartite multidrug efflux pump EA
Map data
Sample
  • Complex: EmrAB-TolC
    • Protein or peptide: Multidrug export protein EmrA
  • Protein or peptide: Outer membrane protein TolC
  • Protein or peptide: Multidrug export protein EmrB
KeywordsSTRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsDu D / Zhong Z / Tuerxunjiang M
Funding support China, 1 items
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, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39879.png

Downloads & links

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Map

FileDownload / File: emd_39879.map.gz / Format: CCP4 / Size: 244.1 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.)
1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.006272217 - 1.8081024
Average (Standard dev.)0.00084149005 (±0.022026004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39879_msk_1.map
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Half map: #2

Fileemd_39879_half_map_1.map
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Half map: #1

Fileemd_39879_half_map_2.map
Projections & Slices
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Sample components

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Entire : EmrAB-TolC

EntireName: EmrAB-TolC
Components
  • Complex: EmrAB-TolC
    • Protein or peptide: Multidrug export protein EmrA
  • Protein or peptide: Outer membrane protein TolC
  • Protein or peptide: Multidrug export protein EmrB

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Supramolecule #1: EmrAB-TolC

SupramoleculeName: EmrAB-TolC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Multidrug export protein EmrA

MacromoleculeName: Multidrug export protein EmrA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 37.594523 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: RHFEETDDAY VAGNQIQIMS QVSGSVTKVW ADNTDFVKEG DVLVTLDPTD ARQAFEKAKT ALASSVRQTH QLMINSKQLQ ANIEVQKIA LAKAQSDYNR RVPLGNANLI GREELQHARD AVTSAQAQLD VAIQQYNANQ AMILGTKLED QPAVQQAATE V RNAWLALE ...String:
RHFEETDDAY VAGNQIQIMS QVSGSVTKVW ADNTDFVKEG DVLVTLDPTD ARQAFEKAKT ALASSVRQTH QLMINSKQLQ ANIEVQKIA LAKAQSDYNR RVPLGNANLI GREELQHARD AVTSAQAQLD VAIQQYNANQ AMILGTKLED QPAVQQAATE V RNAWLALE RTRIISPMTG YVSRRAVQPG AQISPTTPLM AVVPATNMWV DANFKETQIA NMRIGQPVTI TTDIYGDDVK YT GKVVGLD MGTGSAFSLL PAQNATGNWI KVVQRLPVRI ELDQKQLEQY PLRIGLSTLV SVNTTNRDGQ VLANKVRSTP VAV STAREI SLAPVNKLID DIVKANAG

UniProtKB: Multidrug export protein EmrA

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Macromolecule #2: Outer membrane protein TolC

MacromoleculeName: Outer membrane protein TolC / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 47.00384 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: ENLMQVYQQA RLSNPELRKS AADRDAAFEK INEARSPLLP QLGLGADYTY SNGYRDANGI NSNATSASLQ LTQSIFDMSK WRALTLQEK AAGIQDVTYQ TDQQTLILNT ATAYFNVLNA IDVLSYTQAQ KEAIYRQLDQ TTQRFNVGLV AITDVQNARA Q YDTVLANE ...String:
ENLMQVYQQA RLSNPELRKS AADRDAAFEK INEARSPLLP QLGLGADYTY SNGYRDANGI NSNATSASLQ LTQSIFDMSK WRALTLQEK AAGIQDVTYQ TDQQTLILNT ATAYFNVLNA IDVLSYTQAQ KEAIYRQLDQ TTQRFNVGLV AITDVQNARA Q YDTVLANE LTARNNLDNA VEQLRQITGN YYPELAALNV ENFKTDKPQP VNALLKEAEK RNLSLLQARL SQDLAREQIR QA QDGHLPT LDLTASTGIS DTSYSGSKTR GAAGTQYDDS NMGQNKVGLS FSLPIYQGGM VNSQVKQAQY NFVGASEQLE SAH RSVVQT VRSSFNNINA SISSINAYKQ AVVSAQSSLD AMEAGYSVGT RTIVDVLDAT TTLYNAKQEL ANARYNYLIN QLNI KSALG TLNEQDLLAL NNALSKPVST NPE

UniProtKB: Outer membrane protein TolC

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Macromolecule #3: Multidrug export protein EmrB

MacromoleculeName: Multidrug export protein EmrB / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 53.991133 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: AQLVIMTIAL SLATFMQVLD STIANVAIPT IAGNLGSSLS QGTWVITSFG VANAISIPLT GWLAKRVGEV KLFLWSTIAF AIASWACGV SSSLNMLIFF RVIQGIVAGP LIPLSQSLLL NNYPPAKRSI ALALWSMTVI VAPICGPILG GYISDNYHWG W IFFINVPI ...String:
AQLVIMTIAL SLATFMQVLD STIANVAIPT IAGNLGSSLS QGTWVITSFG VANAISIPLT GWLAKRVGEV KLFLWSTIAF AIASWACGV SSSLNMLIFF RVIQGIVAGP LIPLSQSLLL NNYPPAKRSI ALALWSMTVI VAPICGPILG GYISDNYHWG W IFFINVPI GVAVVLMTLQ TLRGRETRTE RRRIDAVGLA LLVIGIGSLQ IMLDRGKELD WFSSQEIIIL TVVAVVAICF LI VWELTDD NPIVDLSLFK SRNFTIGCLC ISLAYMLYFG AIVLLPQLLQ EVYGYTATWA GLASAPVGII PVILSPIIGR FAH KLDMRR LVTFSFIMYA VCFYWRAYTF EPGMDFGASA WPQFIQGFAV ACFFMPLTTI TLSGLPPERL AAASSLSNFT RTLA GSIGT SITTTMWTNR ESMHHAQLTE SVNPFNPNAQ AMYSQLEGLG MTQQQASGWI AQQITNQGLI ISANEIFWMS AGIFL VLLG LVWFAKPPFG

UniProtKB: Multidrug export protein EmrB

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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

Concentration0.7 mg/mL
BufferpH: 7.5
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19180
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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