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- EMDB-29694: BceAB-S nucleotide free BceS state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-29694
TitleBceAB-S nucleotide free BceS state 1
Map dataFinal map
Sample
  • Complex: BceAB-S
    • Protein or peptide: Bacitracin export permease protein BceB
    • Protein or peptide: Bacitracin export ATP-binding protein BceA
    • Protein or peptide: Sensor protein BceS
  • Ligand: PALMITIC ACID
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: OLEIC ACID
KeywordsABC transporter / histidine kinase / antimicrobial / 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 family / 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 family / 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 / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Histidine kinase/HSP90-like ATPase superfamily / 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: 3.7 Å
AuthorsGeorge NL / 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: Nat Commun / Year: 2023
Title: Architecture of a complete Bce-type antimicrobial peptide resistance module.
Authors: Natasha L George / Benjamin J Orlando /
Abstract: Gram-positive bacteria synthesize and secrete antimicrobial peptides that target the essential process of peptidoglycan synthesis. These antimicrobial peptides not only regulate the dynamics of ...Gram-positive bacteria synthesize and secrete antimicrobial peptides that target the essential process of peptidoglycan synthesis. These antimicrobial peptides not only regulate the dynamics of microbial communities but are also of clinical importance as exemplified by peptides such as bacitracin, vancomycin, and daptomycin. Many gram-positive species have evolved specialized antimicrobial peptide sensing and resistance machinery known as Bce modules. These modules are membrane protein complexes formed by an unusual Bce-type ABC transporter interacting with a two-component system sensor histidine kinase. In this work, we provide the first structural insight into how the membrane protein components of these modules assemble into a functional complex. A cryo-EM structure of an entire Bce module revealed an unexpected mechanism of complex assembly, and extensive structural flexibility in the sensor histidine kinase. Structures of the complex in the presence of a non-hydrolysable ATP analog reveal how nucleotide binding primes the complex for subsequent activation. Accompanying biochemical data demonstrate how the individual membrane protein components of the complex exert functional control over one another to create a tightly regulated enzymatic system.
History
DepositionFeb 7, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29694.png

Downloads & links

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Map

FileDownload / File: emd_29694.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.92 Å		0.87 Å/pix.
x 360 pix.
= 313.92 Å		0.87 Å/pix.
x 360 pix.
= 313.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.872 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.58943075 - 0.93519133
Average (Standard dev.)0.0011454108 (±0.0150680775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29694_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_29694_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_29694_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_29694_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Sample components

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Entire : BceAB-S

EntireName: BceAB-S
Components
  • Complex: BceAB-S
    • Protein or peptide: Bacitracin export permease protein BceB
    • Protein or peptide: Bacitracin export ATP-binding protein BceA
    • Protein or peptide: Sensor protein BceS
  • Ligand: PALMITIC ACID
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: OLEIC ACID

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Supramolecule #1: BceAB-S

SupramoleculeName: BceAB-S / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: A membrane protein complex formed by the BceAB transporter and BceS histidine kinase
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 167 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 (E. coli)
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: 29.248377 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGHHHHHHV ILEANKIRKS YGNKLNKQEV LKGIDIHIEK GEFVSIMGAS GSGKTTLLNV LSSIDQVSHG TIHINGNDMT AMKEKQLAE FRKQHLGFIF QDYNLLDTLT VKENILLPLS ITKLSKKEAN RKFEEVAKEL GIYELRDKYP NEISGGQKQR T SAGRAFIH ...String:
MSGHHHHHHV ILEANKIRKS YGNKLNKQEV LKGIDIHIEK GEFVSIMGAS GSGKTTLLNV LSSIDQVSHG TIHINGNDMT AMKEKQLAE FRKQHLGFIF QDYNLLDTLT VKENILLPLS ITKLSKKEAN RKFEEVAKEL GIYELRDKYP NEISGGQKQR T SAGRAFIH DPSIIFADEP TGALDSKSAS DLLNKLSQLN QKRNATIIMV THDPVAASYC GRVIFIKDGQ MYTQLNKGGQ DR QTFFQDI MKTQGVLGGV QHEH

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 (E. coli)
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: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #5: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 5 / Number of copies: 2 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Macromolecule #6: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID

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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

Concentration6.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMTris
0.005 %LMNG

Details: 150mM NaCl, 25mM Tris-HCl, 0.005% LMNG
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.5 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: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120730
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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