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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: To Be Published
Title: Structural Analysis of a Mechanotransmission ABC Transporter Induced By Cell Wall Targeting Antibiotics
Authors: Yu, P. / Krah, B.S. / Orlando, M.A. / Orlando, B.J.
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: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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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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