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- EMDB-66536: Cryo-EM structure of Streptococcus thermophilus FoeAB in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66536
TitleCryo-EM structure of Streptococcus thermophilus FoeAB in complex with ATP and ADP
Map data
Sample
  • Complex: FoeAB
    • Protein or peptide: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
    • Protein or peptide: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type oligopeptide transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein / Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsTaguchi A / Fujita J / Namba K / Nishino K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K14518 Japan
Other private Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural insights into fosfomycin efflux by a streptococcal ABC transporter.
Authors: Atsushi Taguchi / Junso Fujita / Mikio Tanabe / Daisuke Takaya / Kazuo Harada / Toshio Moriya / Kaori Fukuzawa / Keiichi Namba / Kunihiko Nishino /
Abstract: Gram-positive bacteria encode a broad array of ABC transporters that mediate substrate translocation across the cell membrane, with some contributing to their survival under environmental stresses ...Gram-positive bacteria encode a broad array of ABC transporters that mediate substrate translocation across the cell membrane, with some contributing to their survival under environmental stresses such as antimicrobial exposure. While several of these transporters have been shown to exhibit multidrug efflux activity, the functional roles of many others remain unknown. Here, using an efflux pump screen in the opportunistic human pathogen , we identified a previously uncharacterized type IV ABC transporter (FoeAB) that confers resistance to the antibiotic fosfomycin. We show that purified FoeAB mediates fosfomycin transport in a liposome-reconstituted system and provide evidence that it functions as a multidrug efflux pump with substrate preferences distinct from those of known efflux pumps. Furthermore, we present cryogenic electron microscopy (cryo-EM) structures of FoeAB in inward- and outward-facing states, which reveal conformational changes associated with nucleotide binding and identify residues important for substrate transport. Collectively, these findings expand the known repertoire of antibiotic-exporting ABC transporters in Gram-positive bacteria and provide structural insight into the underlying transport mechanism.
History
DepositionOct 10, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66536.png

Downloads & links

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Map

FileDownload / File: emd_66536.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 300 pix.
= 309.6 Å		1.03 Å/pix.
x 300 pix.
= 309.6 Å		1.03 Å/pix.
x 300 pix.
= 309.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.032 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.5208383 - 2.430602
Average (Standard dev.)0.00056640676 (±0.043479923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 309.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66536_msk_1.map
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Half map: #2

Fileemd_66536_half_map_1.map
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Half map: #1

Fileemd_66536_half_map_2.map
Projections & Slices
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Sample components

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Entire : FoeAB

EntireName: FoeAB
Components
  • Complex: FoeAB
    • Protein or peptide: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
    • Protein or peptide: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: FoeAB

SupramoleculeName: FoeAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Streptococcus thermophilus (bacteria)

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Macromolecule #1: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-s...

MacromoleculeName: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus thermophilus (bacteria)
Molecular weightTheoretical: 67.879664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKALLVYFKG FVKDSILGPV FKLIEASFEL LVPMVIAGIV DITIPNRDQN HLFMMIFLLF GLAVIGVVVA ISAQYFSSRA AVGYAQALT NDLYAKIMRL SKEKRDEIGT SSLVTRLTGD TFQIQTGINQ FLRLFLRAPI IVTGAIIMAF RISPRLTLWF I GMVLVLSL ...String:
MKALLVYFKG FVKDSILGPV FKLIEASFEL LVPMVIAGIV DITIPNRDQN HLFMMIFLLF GLAVIGVVVA ISAQYFSSRA AVGYAQALT NDLYAKIMRL SKEKRDEIGT SSLVTRLTGD TFQIQTGINQ FLRLFLRAPI IVTGAIIMAF RISPRLTLWF I GMVLVLSL IIVLASRIVN PLYAKIRLIN ESIVTNTRQQ LEGMRVIRAF GQSERELDNF TTVNKELKKW QLKTGVISSL IS PLTFLVV NMTLIAILWQ GNVQIQGGLL SQGMLIALVN YLLQILAELL KLAMMLTNLN QSFISAKRVQ AIFNLQDEDI EAP LIIKKP NQPSIALEID KMTFTYPTAS QPSLQEIDFK TFEGESLGII GGTGSGKSTL VNLIMNLYKP QFGSLTIFKN QLSP NNLKE WRSWVAYVPQ KAELFRGTIR SNLSLGLDYE PSDQELWHAL DMAQASDFVR EKELGLDEPV ESFGRNFSGG QRQRL TIAR ALMRPAPFLI LDDSTSALDY LTESRLLAAI RENLKSTSLI IISQRPNSLK AVDQILVLDK GHQVGLGNHE ELLATN KIY QDIHYSQHQK VVADEGGSAW SHPQFEKGGG SGGGSGGSAW SHPQLEK

UniProtKB: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein

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Macromolecule #2: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-s...

MacromoleculeName: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus thermophilus (bacteria)
Molecular weightTheoretical: 65.864094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKARNNKSTL KRLCKDILSQ CYLFALATVG TIVQVALTVY FPILLGDAVD AVLKMNAVFL MSRLIWQMLL LILANSAIQW LNPLIYNRL IYSYSESLRE RVMMKIHAIP FSYLDRQGTG DMVSRVTTDS DQLNNGLLMF FNQFFVGLLT IFVIIITMAR L DWFMMLLV ...String:
MKARNNKSTL KRLCKDILSQ CYLFALATVG TIVQVALTVY FPILLGDAVD AVLKMNAVFL MSRLIWQMLL LILANSAIQW LNPLIYNRL IYSYSESLRE RVMMKIHAIP FSYLDRQGTG DMVSRVTTDS DQLNNGLLMF FNQFFVGLLT IFVIIITMAR L DWFMMLLV LVMTPLSMLV TRFIARKSYQ LYRNQTKWRG KQTQLIEESL TQEALVQILN AQDQMVRNFN EVNGKYANYS QG AIFYSSA VNPATRFFNS LLYALITGVG AYRIMSGGTF TVGQLTTFLN YVTQYTKPFN DISSVLSELQ SALACADRLY MIL DEDEIP ETGNAVLDEA EVQGHFQFDH VQFGYLQNKP LIKDLSIDIP AASTVAIVGP TGAGKSTLIN LLMRFYDLDK GQIL LDGRD ITYYTRESLR KQIGMVLQET WLKVATIHDN IAYGNPKASR EEVVAAAKAA NADFFIKQLP LGYDTFLKDA GQSLS QGQR QLLTIARIFV NVPKILILDE ATSSIDTRTE LLIQEAFAKL MKGRTSFIIA HRLSTIENAD LILVMNNGDI VEHGTH NQL MRTKGMYYRM QTAQKTQNN

UniProtKB: Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration3.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
0.02 %DDMn-Dodecyl-beta-D-maltoside
1.0 mMATPadenosine triphosphate
1.0 mMMgCl2magnesium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.3 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3870986
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 430550
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9x4b:
Cryo-EM structure of Streptococcus thermophilus FoeAB in complex with ATP and ADP

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