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- EMDB-66953: Cryo-EM structure of Streptococcus thermophilus FoeAB in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66953
TitleCryo-EM structure of Streptococcus thermophilus FoeAB in complex with AMPPNP
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: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordsfosfomycin / ABC transporter / TRANSPORT 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: 2.9 Å
AuthorsTanabe M / Taguchi A / Moriya T / Nishino K
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K20759 Japan
Japan Society for the Promotion of Science (JSPS)23K14518 Japan
Japan Society for the Promotion of Science (JSPS)25K02496 Japan
Japan Agency for Medical Research and Development (AMED)JP23nk0101653 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121001 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121030, Japan
CitationJournal: To Be Published
Title: Structural insights into fosfomycin efflux by a streptococcal ABC transporter
Authors: Taguchi A / Fujita J / Tanabe M / Takaya D / Harada K / Moriya T / Fukuzawa K / Namba K / Nishino K
History
DepositionNov 5, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66953.png

Downloads & links

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Map

FileDownload / File: emd_66953.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 324 pix.
= 268.92 Å		0.83 Å/pix.
x 324 pix.
= 268.92 Å		0.83 Å/pix.
x 324 pix.
= 268.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.042492133 - 0.0743833
Average (Standard dev.)-0.00014426406 (±0.00211251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 268.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66953_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66953_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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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 B (bacteria)
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 B (bacteria)
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: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Details: 20mM HEPES pH7.5, 150mM NaCl, 5mM MgCl2, 5mM AMP-PNP, 10mM drug fosfomycin, 0.025% DDM
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6918 / Average electron dose: 50.0 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: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3059472
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 245983
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 144500
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9xka:
Cryo-EM structure of Streptococcus thermophilus FoeAB in complex with AMPPNP

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