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- PDB-9o9y: Bacillus ytrEF vanadate trapped conformation -

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Basic information

Entry
Database: PDB / ID: 9o9y
TitleBacillus ytrEF vanadate trapped conformation
Components(ABC transporter ...) x 2
KeywordsMEMBRANE PROTEIN / ABC Transporter / vanadate / ATP
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
ADENOSINE-5'-DIPHOSPHATE / Unknown ligand / VANADATE ION / ABC transporter ATP-binding protein YtrE / ABC transporter permease YtrF
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsYu, P. / Krah, B.S. / Orlando, M.A. / Orlando, B.J.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ABC transporter ATP-binding protein YtrE
D: ABC transporter permease YtrF
C: ABC transporter permease YtrF
A: ABC transporter ATP-binding protein YtrE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,41812
Polymers152,2854
Non-polymers1,1338
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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ABC transporter ... , 2 types, 4 molecules BADC

#1: Protein ABC transporter ATP-binding protein YtrE


Mass: 27664.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct has a HIS tag and a thrombin cleavage site in the N terminal of ytrE.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: Strain 168 / Gene: ytrE, BSU30420 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O34392
#2: Protein ABC transporter permease YtrF


Mass: 48477.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ytrF, BSU30410 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O35005

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacillus ABC transporter ytrEF in vanadate-bound conformation
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria) / Strain: C41 / Plasmid: pET28a
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM4-(2-Hydroxyethyl)piperazine-1-ethane-sulfonic acidHEPES1
2150 mMSodium chlorideNACl1
35 mM2-HydroxyethylmercaptanBME1
40.005 %lauryl maltose neopentyl glycolLMNG1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The ytrEF in nucleotide-free conformation is mono disperse and pure before plunge-frozen onto the cryoEM grids.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44.34 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11530
EM imaging opticsEnergyfilter name: TFS Selectris

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.1particle selection
4cryoSPARC4.4.1CTF correctionPatch CTF estimation
7UCSF Chimera1.16model fitting
9cryoSPARC4.4.1initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
11cryoSPARC4.4.1classification
12cryoSPARC4.4.13D reconstruction
13PHENIX1.21.2_5419model refinement
Image processingDetails: The images were corrected for beam induced motion using patch motion correction in cryoSPARC.
CTF correctionDetails: Patch CTF estimation was performed in cryoSPARC. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9246031
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 652937 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: Refinement in phenix.real_space_refine
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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