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- EMDB-19734: BceABS nucleotide-free state -

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Basic information

Entry
Database: EMDB / ID: EMD-19734
TitleBceABS nucleotide-free state
Map datarefinement volume of full complex
Sample
  • Complex: Detergent solubilised BceABS complex.
    • Protein or peptide: Bacitracin export permease protein BceB
    • Protein or peptide: Bacitracin export ATP-binding protein BceA
    • Protein or peptide: Sensor protein BceS
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CARDIOLIPIN
KeywordsABC transporter / bacitracin resistance / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein histidine kinase activity / histidine kinase / phosphorelay signal transduction system / transmembrane transporter activity / transmembrane transport / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter permease protein, BceB-type / : / : / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...ABC transporter permease protein, BceB-type / : / : / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 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
Bacitracin export ATP-binding protein BceA / Bacitracin export permease protein BceB / Sensor protein BceS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMcAndrew MBL / Brotherton DH / Crow A
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N014294/1 United Kingdom
CitationJournal: To Be Published
Title: BceABS nucleotide-free state
Authors: McAndrew MBL / Brotherton DH / Stansfeld PJ / Crow A
History
DepositionFeb 23, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19734.png

Downloads & links

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Map

FileDownload / File: emd_19734.map.gz / Format: CCP4 / Size: 316.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefinement volume of full complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 436 pix.
= 364.06 Å		0.84 Å/pix.
x 436 pix.
= 364.06 Å		0.84 Å/pix.
x 436 pix.
= 364.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00328
Minimum - Maximum-0.015687043 - 0.03238505
Average (Standard dev.)0.00003407442 (±0.00049968367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions436436436
Spacing436436436
CellA=B=C: 364.06 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened refinement

Fileemd_19734_additional_1.map
Annotationunsharpened refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: refinement volume of full complex

Fileemd_19734_half_map_1.map
Annotationrefinement volume of full complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: refinement volume of full complex

Fileemd_19734_half_map_2.map
Annotationrefinement volume of full complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Detergent solubilised BceABS complex.

EntireName: Detergent solubilised BceABS complex.
Components
  • Complex: Detergent solubilised BceABS complex.
    • Protein or peptide: Bacitracin export permease protein BceB
    • Protein or peptide: Bacitracin export ATP-binding protein BceA
    • Protein or peptide: Sensor protein BceS
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CARDIOLIPIN

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Supramolecule #1: Detergent solubilised BceABS complex.

SupramoleculeName: Detergent solubilised BceABS complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Bacitracin export permease protein BceB

MacromoleculeName: Bacitracin export permease protein BceB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 72.262109 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNINQLILRN LKKNLRNYYL YVFALIFSVA LYFAFVTLQY DPAINEVKAS IKGAAAIKTA SILLVAVVAI FILYANTIFI KRRSKEIGL FQLIGMTKHK IFRILSAENV MLYFGSLAIG VAAGFSISKL VLMILFKIVD VKADAKLHFS EQALVQTVIV F CGIYLLIM ...String:
MNINQLILRN LKKNLRNYYL YVFALIFSVA LYFAFVTLQY DPAINEVKAS IKGAAAIKTA SILLVAVVAI FILYANTIFI KRRSKEIGL FQLIGMTKHK IFRILSAENV MLYFGSLAIG VAAGFSISKL VLMILFKIVD VKADAKLHFS EQALVQTVIV F CGIYLLIM IMNYTFIKKQ SILSLFKVTS STEDKVKKIS FFQMLIGALG IVLILTGYYV SSELFGGKFK TINELFVAMS FI LGSVIIG TFLFYKGSVT FISNIIRKSK GGYLNISEVL SLSSIMFRMK SNALLLTIIT TVSALAIGLL SLAYISYYSS EKT AEQNVA ADFSFMNEKD AKLFENKLRE SNISFVKKAT PVLQANVDIA NIMDGTPKEM QGDPGNMQLA VVSDKDVKGV DVAA GEAVF SGYTDLLQKI MVFKDSGVIK VKSKHETQPL KYKGLREEFL VSYTFTSGGM PAVIVDDSLF KQLDKDKDPR IQLAQ STFI GVNVKHDDQM EKANELFQQV NKKNEHLSRL DTSAAQKSLF GMVMFIVGFL GLTFLITSGC ILYFKQMGES EDEKPS YTI LRKLGFTQGD LIKGIRIKQM YNFGIPLVVG LFHSYFAVQS GWFLFGSEVW APMIMVMVLY TALYSIFGFL SVLYYKK VI KSSL

UniProtKB: Bacitracin export permease protein BceB

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Macromolecule #2: Bacitracin export ATP-binding protein BceA

MacromoleculeName: Bacitracin export ATP-binding protein BceA / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 30.446725 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MVILEANKIR KSYGNKLNKQ EVLKGIDIHI EKGEFVSIMG ASGSGKTTLL NVLSSIDQVS HGTIHINGN DMTAMKEKQL AEFRKQHLGF IFQDYNLLDT LTVKENILLP LSITKLSKKE ANRKFEEVAK ELGIYELRDK Y PNEISGGQ ...String:
MGSSHHHHHH SSGLVPRGSH MVILEANKIR KSYGNKLNKQ EVLKGIDIHI EKGEFVSIMG ASGSGKTTLL NVLSSIDQVS HGTIHINGN DMTAMKEKQL AEFRKQHLGF IFQDYNLLDT LTVKENILLP LSITKLSKKE ANRKFEEVAK ELGIYELRDK Y PNEISGGQ KQRTSAGRAF IHDPSIIFAD EPTGALDSKS ASDLLNKLSQ LNQKRNATII MVTHDPVAAS YCGRVIFIKD GQ MYTQLNK GGQDRQTFFQ DIMKTQGVLG GVQHEH

UniProtKB: Bacitracin export ATP-binding protein BceA

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Macromolecule #3: Sensor protein BceS

MacromoleculeName: Sensor protein BceS / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 38.811898 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIKAFLIERR SWIAAFLFQQ ALMLFIAFVD PSISFGNVLY MVYLCILFFI IFLWFRYRKE TAFYKSLKTW ENNLDVTAIN EPETPFEAM VERSIAGQTE HLKQTAARHR LALENEKDEL MAWIHEVKTP LTAMHLIIDR MEEKALKSQL SYEWLRIHLL L DQQLHQKR ...String:
MIKAFLIERR SWIAAFLFQQ ALMLFIAFVD PSISFGNVLY MVYLCILFFI IFLWFRYRKE TAFYKSLKTW ENNLDVTAIN EPETPFEAM VERSIAGQTE HLKQTAARHR LALENEKDEL MAWIHEVKTP LTAMHLIIDR MEEKALKSQL SYEWLRIHLL L DQQLHQKR ISFIENDLSV EFIQLQPLIF KEIKDLQSWC IQKGIGFDIQ LEAKEVLSDA KWLAFIIRQL LTNAVKYSEA SE IEIKSFQ KGEQTQLQVK DCGRGIDPKD VPRIFDKGFT STTDHHDQAS TGMGLYLAKK AAAPLLIHID VESEFGAGTV FTL TFPIRN QFEHVISV

UniProtKB: Sensor protein BceS

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #5: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 5 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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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

Concentration1.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
165.0 mMNaClsodium chloride
20.0 mMHEPESHEPES buffer
0.005 %LMNGLauryl Maltose Neopentyl Glycol

Details: 20mM HEPES pH 8.0, 150mM NaCl, made up to 165mM at the point of freezing, 0.005% LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 35mA glow discharge
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV
Detailsmono disperse from size exclusion

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9038 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 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: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4778215
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Software - details: as implemented in Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5-beta) / Number images used: 940216
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8s5g:
BceABS nucleotide-free state

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