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- EMDB-25812: BceAB E169Q variant ATP-bound conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-25812
TitleBceAB E169Q variant ATP-bound conformation
Map dataCryo-EM map of BceAB in an ATP-bound conformation
Sample
  • Complex: BceAB (E169Q variant)
    • Protein or peptide: Bacitracin export permease protein BceB
    • Protein or peptide: Bacitracin export ATP-binding protein BceA
  • Ligand: 4-amino-4-deoxy-1-O-[(S)-hydroxy{[(2E,6E,10Z,14Z,18Z,22E,26E,30E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-yl]oxy}phosphoryl]-alpha-L-arabinopyranose
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsBceAB / bacitracin / transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


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 / 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
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 support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Conformational snapshots of the bacitracin sensing and resistance transporter BceAB.
Authors: Natasha L George / Anthony L Schilmiller / Benjamin J Orlando /
Abstract: SignificanceMany gram-positive organisms have evolved an elegant solution to sense and resist antimicrobial peptides that inhibit cell-wall synthesis. These organisms express an unusual "Bce-type" ...SignificanceMany gram-positive organisms have evolved an elegant solution to sense and resist antimicrobial peptides that inhibit cell-wall synthesis. These organisms express an unusual "Bce-type" adenosine triphosphate-binding cassette (ABC) transporter that recognizes complexes formed between antimicrobial peptides and lipids involved in cell-wall biosynthesis. In this work, we provide the first structural snapshots of a Bce-type ABC transporter trapped in different conformational states. Our structures and associated biochemical data provide key insights into the novel target protection mechanism that these unusual ABC transporters use to sense and resist antimicrobial peptides. The studies described herein set the stage to begin developing a comprehensive molecular understanding of the diverse interactions between antimicrobial peptides and conserved resistance machinery found across most gram-positive organisms.
History
DepositionDec 23, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25812.png

Downloads & links

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Map

FileDownload / File: emd_25812.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of BceAB in an ATP-bound conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261.6 Å		0.87 Å/pix.
x 300 pix.
= 261.6 Å		0.87 Å/pix.
x 300 pix.
= 261.6 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: 0.11
Minimum - Maximum-0.82818884 - 1.1552622
Average (Standard dev.)-0.00023431359 (±0.026334485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A

Fileemd_25812_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_25812_half_map_2.map
AnnotationHalf-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 : BceAB (E169Q variant)

EntireName: BceAB (E169Q variant)
Components
  • Complex: BceAB (E169Q variant)
    • Protein or peptide: Bacitracin export permease protein BceB
    • Protein or peptide: Bacitracin export ATP-binding protein BceA
  • Ligand: 4-amino-4-deoxy-1-O-[(S)-hydroxy{[(2E,6E,10Z,14Z,18Z,22E,26E,30E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-yl]oxy}phosphoryl]-alpha-L-arabinopyranose
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: BceAB (E169Q variant)

SupramoleculeName: BceAB (E169Q variant) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 129 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)
Strain: 168
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)
Strain: 168
Molecular weightTheoretical: 29.247393 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 DPSIIFADQP TGALDSKSAS DLLNKLSQLN QKRNATIIMV THDPVAASYC GRVIFIKDGQ MYTQLNKGGQ DR QTFFQDI MKTQGVLGGV QHEH

UniProtKB: Bacitracin export ATP-binding protein BceA

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Macromolecule #3: 4-amino-4-deoxy-1-O-[(S)-hydroxy{[(2E,6E,10Z,14Z,18Z,22E,26E,30E)...

MacromoleculeName: 4-amino-4-deoxy-1-O-[(S)-hydroxy{[(2E,6E,10Z,14Z,18Z,22E,26E,30E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-yl]oxy}phosphoryl]-alpha-L-arabinopyranose
type: ligand / ID: 3 / Number of copies: 1 / Formula: I0O
Molecular weightTheoretical: 842.178 Da
Chemical component information

ChemComp-I0O:
4-amino-4-deoxy-1-O-[(S)-hydroxy{[(2E,6E,10Z,14Z,18Z,22E,26E,30E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-yl]oxy}phosphoryl]-alpha-L-arabinopyranose

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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

Concentration7 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMsodium chlorideNaCl
0.005 %LMNG
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA in Pelco EasyGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.1 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 305229
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7tch:
BceAB E169Q variant ATP-bound conformation

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