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- EMDB-66534: Cryo-EM structure of nucleotide-free Streptococcus thermophilus F... -

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Basic information

Entry
Database: EMDB / ID: EMD-66534
TitleCryo-EM structure of nucleotide-free Streptococcus thermophilus FoeAB 3
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
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: 3.34 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: To Be Published
Title: Structural insights into fosfomycin efflux by a streptococcal ABC transporter
Authors: Taguchi A / Fujita J / Namba K / Nishino K
History
DepositionOct 10, 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_66534.png

Downloads & links

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Map

FileDownload / File: emd_66534.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.032 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.7525208 - 1.2185082
Average (Standard dev.)0.0006754316 (±0.025386617)
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_66534_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66534_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_66534_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

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Supramolecule #1: FoeAB

SupramoleculeName: FoeAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 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
4.0 mMMgCl2magnesium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / 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: 3.0 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: 341371
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: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 43726
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-9x49:
Cryo-EM structure of nucleotide-free Streptococcus thermophilus FoeAB 3

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