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- EMDB-70266: Bacillus ytrEF vanadate trapped conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-70266
TitleBacillus ytrEF vanadate trapped conformation
Map dataA main cryoEM map with sharpening factor of -101.5. The resolution of this map is 2.4 angstrom at a FSC threshold of 0.143.
Sample
  • Complex: Bacillus ABC transporter ytrEF in vanadate-bound conformation
    • Protein or peptide: ABC transporter ATP-binding protein YtrE
    • Protein or peptide: ABC transporter permease YtrF
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: UNKNOWN LIGAND
KeywordsABC Transporter / vanadate / ATP / MEMBRANE PROTEIN
Function / homology
Function and homology information


transmembrane transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / 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. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding protein YtrE / ABC transporter permease YtrF
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsYu P / Krah BS / Orlando MA / Orlando BJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM146721 United States
CitationJournal: Structure / Year: 2025
Title: Structural analysis of a Gram-positive type VII ABC transporter induced by cell wall-targeting antibiotics.
Authors: Peixuan Yu / Bradon S Krah / Melanie A Orlando / Sundharraman Subramanian / Benjamin J Orlando /
Abstract: Bacteria utilize a variety of mechanisms to remodel the cell wall in response to environmental and antimicrobial stress. In the model organism Bacillus subtilis, the ytr operon encoding putative ATP- ...Bacteria utilize a variety of mechanisms to remodel the cell wall in response to environmental and antimicrobial stress. In the model organism Bacillus subtilis, the ytr operon encoding putative ATP-binding cassette (ABC) transporter(s) is highly upregulated in response to cell wall-targeting antibiotics. Here we show that the ytr operon encodes two distinct ABC transporters: YtrBCD and YtrEF. Using cryo-electron microscopy(cryo-EM), we determined the structures of YtrEF in nucleotide-free and ADP-vanadate bound states. The structures demonstrate that YtrEF adopts a type VII ABC transporter fold. Nucleotide binding induced conformational changes that propagate from the cytosolic region through the transmembrane helices to ultimately reorient the extracellular domains. Extended bacterial growth assays and suppressor mutation identification indicated that YtrEF contributes to alteration of colony morphology. These findings establish YtrEF as a type VII ABC transporter that is induced by cell wall-targeting antibiotics and a new avenue to phenotypically assess the ytr operon.
History
DepositionApr 18, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70266.png

Downloads & links

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Map

FileDownload / File: emd_70266.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA main cryoEM map with sharpening factor of -101.5. The resolution of this map is 2.4 angstrom at a FSC threshold of 0.143.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 320 pix.
= 283.52 Å		0.89 Å/pix.
x 320 pix.
= 283.52 Å		0.89 Å/pix.
x 320 pix.
= 283.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.886 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0438
Minimum - Maximum-0.9548073 - 1.9286958
Average (Standard dev.)0.00004348556 (±0.021797836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 283.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: A cryoEM map derived from DeepEMhancer algorithm.

Fileemd_70266_additional_1.map
AnnotationA cryoEM map derived from DeepEMhancer algorithm.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened cryoEM map

Fileemd_70266_additional_2.map
Annotationunsharpened cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unsharpened cryoEM map A

Fileemd_70266_half_map_1.map
Annotationunsharpened cryoEM map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unsharpened cryoEM map B

Fileemd_70266_half_map_2.map
Annotationunsharpened cryoEM map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus ABC transporter ytrEF in vanadate-bound conformation

EntireName: Bacillus ABC transporter ytrEF in vanadate-bound conformation
Components
  • Complex: Bacillus ABC transporter ytrEF in vanadate-bound conformation
    • Protein or peptide: ABC transporter ATP-binding protein YtrE
    • Protein or peptide: ABC transporter permease YtrF
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: UNKNOWN LIGAND

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Supramolecule #1: Bacillus ABC transporter ytrEF in vanadate-bound conformation

SupramoleculeName: Bacillus ABC transporter ytrEF in vanadate-bound conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: ABC transporter ATP-binding protein YtrE

MacromoleculeName: ABC transporter ATP-binding protein YtrE / type: protein_or_peptide / ID: 1
Details: The construct has a HIS tag and a thrombin cleavage site in the N terminal of ytrE.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: Strain 168
Molecular weightTheoretical: 27.664412 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MIDVQHIDHS FTIGKKGREN EVPVLKDVSL SVAKGEIACI VGRSGSGKST LLNLISGYIS PTKGRIVIN GTDVTGFNEK EWAQFRLDHF GFIFQSFQLI PGLTTYENVE MPLALKGIKP SERKQKVQDM LKRVGLENHA A HYPNELSG ...String:
MGSSHHHHHH SSGLVPRGSH MIDVQHIDHS FTIGKKGREN EVPVLKDVSL SVAKGEIACI VGRSGSGKST LLNLISGYIS PTKGRIVIN GTDVTGFNEK EWAQFRLDHF GFIFQSFQLI PGLTTYENVE MPLALKGIKP SERKQKVQDM LKRVGLENHA A HYPNELSG GQQQRVSIAR ALILNPSIIL ADEPTGSLDS ETEHEVLELI QQLNRERGIT FVIITHDDEV ASIGHSKFQL HD GVLKGGI TVEV

UniProtKB: ABC transporter ATP-binding protein YtrE

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Macromolecule #2: ABC transporter permease YtrF

MacromoleculeName: ABC transporter permease YtrF / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 48.477973 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRFKDQVHFI RRNMKKNRLR VFMTILATTM ACAFLVVLSS VGFGIQKTIT DMTMSQQIVT KVSVMGKEGD KPIKKADLEK YDHVRSVVE RTQVYEPNKA TLGNRTNESS NLIFTNMNDE LKANMELEKG RVAKSENEIV VGYDFAKRLL TKKESEEYNK K IEEAKGNP ...String:
MRFKDQVHFI RRNMKKNRLR VFMTILATTM ACAFLVVLSS VGFGIQKTIT DMTMSQQIVT KVSVMGKEGD KPIKKADLEK YDHVRSVVE RTQVYEPNKA TLGNRTNESS NLIFTNMNDE LKANMELEKG RVAKSENEIV VGYDFAKRLL TKKESEEYNK K IEEAKGNP EDIKEPKGYT KDILNKTIEL SVSKTDSKTG DVTKTKTYDF KIVGITKKPS QDWMEDSNIF ISDQFKKDFS EF LDFKGGN VETNIGVFAD KFENVEQLTN DLTDDGYYVT SVTTELEGAN TFFMVFKIGL IFVGCIAVII SAIGIFNTMT MAV TERTQE IGIMKAIGAS PSIIRRMFLM ESAYIGILGC VIGIIISYGV SYLVNLAVPM ILAATSGGDA GDLNYTFSYI PASL VIIAV VICGGVAVIS GMNPARKATK TNVLTALRRE L

UniProtKB: ABC transporter permease YtrF

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #4: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 6 / Number of copies: 2 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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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 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMHEPES4-(2-Hydroxyethyl)piperazine-1-ethane-sulfonic acid
150.0 mMNAClSodium chloride
5.0 mMBME2-Hydroxyethylmercaptan
0.005 %LMNGlauryl maltose neopentyl glycol
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsThe ytrEF in nucleotide-free conformation is mono disperse and pure before plunge-frozen onto the cryoEM grids.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 11530 / Average electron dose: 44.34 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsThe images were corrected for beam induced motion using patch motion correction in cryoSPARC.
Particle selectionNumber selected: 9246031
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Software - details: Patch CTF estimation / Details: Patch CTF estimation was performed in cryoSPARC. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Ab-initio reconstruction were used to generate the initial model.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 652937
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 372987 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsRefinement in phenix.real_space_refine
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9o9y:
Bacillus ytrEF vanadate trapped conformation

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