+Open data
-Basic information
Entry | Database: PDB / ID: 8g3f | ||||||
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Title | BceAB-S nucleotide free BceS state 1 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ABC transporter / histidine kinase / antimicrobial | ||||||
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 | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | George, N.L. / Orlando, B.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g3f.cif.gz | 322.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g3f.ent.gz | 260.6 KB | Display | PDB format |
PDBx/mmJSON format | 8g3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g3f_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8g3f_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8g3f_validation.xml.gz | 66.4 KB | Display | |
Data in CIF | 8g3f_validation.cif.gz | 97.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/8g3f ftp://data.pdbj.org/pub/pdb/validation_reports/g3/8g3f | HTTPS FTP |
-Related structure data
Related structure data | 29694MC 8g3aC 8g3bC 8g3lC 8g4cC 8g4dC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Bacitracin export ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 72262.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: bceB, barD, ytsD, BSU30370 / Production host: Escherichia coli (E. coli) / References: UniProt: O34741 |
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#2: Protein | Mass: 29248.377 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: bceA, barC, ytsC, BSU30380 / Production host: Escherichia coli (E. coli) / References: UniProt: O34697 |
-Protein , 1 types, 2 molecules DE
#3: Protein | Mass: 38811.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: bceS, barB, ytsB, BSU30390 / Production host: Escherichia coli (E. coli) / References: UniProt: O35044, histidine kinase |
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-Non-polymers , 3 types, 4 molecules
#4: Chemical | ChemComp-PLM / | ||
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#5: Chemical | #6: Chemical | ChemComp-OLA / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: BceAB-S / Type: COMPLEX Details: A membrane protein complex formed by the BceAB transporter and BceS histidine kinase Entity ID: #1-#3 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.167 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 8 / Details: 150mM NaCl, 25mM Tris-HCl, 0.005% LMNG | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120730 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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