+Open data
-Basic information
Entry | Database: PDB / ID: 7qfq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Botulinum neurotoxin serotype B | |||||||||
Components | Botulinum neurotoxin type B | |||||||||
Keywords | TOXIN / clostridium botulinum / neurotoxin | |||||||||
Function / homology | Function and homology information Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Clostridium botulinum (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Kosenina, S. / Martinez-Carranza, M. / Davies, J.R. / Masuyer, G. / Stenmark, P. | |||||||||
Funding support | Sweden, 2items
| |||||||||
Citation | Journal: Toxins (Basel) / Year: 2021 Title: Structural Analysis of Botulinum Neurotoxins Type B and E by Cryo-EM. Authors: Sara Košenina / Markel Martínez-Carranza / Jonathan R Davies / Geoffrey Masuyer / Pål Stenmark / Abstract: Botulinum neurotoxins (BoNTs) are the causative agents of a potentially lethal paralytic disease targeting cholinergic nerve terminals. Multiple BoNT serotypes exist, with types A, B and E being the ...Botulinum neurotoxins (BoNTs) are the causative agents of a potentially lethal paralytic disease targeting cholinergic nerve terminals. Multiple BoNT serotypes exist, with types A, B and E being the main cause of human botulism. Their extreme toxicity has been exploited for cosmetic and therapeutic uses to treat a wide range of neuromuscular disorders. Although naturally occurring BoNT types share a common end effect, their activity varies significantly based on the neuronal cell-surface receptors and intracellular SNARE substrates they target. These properties are the result of structural variations that have traditionally been studied using biophysical methods such as X-ray crystallography. Here, we determined the first structures of botulinum neurotoxins using single-particle cryogenic electron microscopy. The maps obtained at 3.6 and 3.7 Å for BoNT/B and /E, respectively, highlight the subtle structural dynamism between domains, and of the binding domain in particular. This study demonstrates how the recent advances made in the field of single-particle electron microscopy can be applied to bacterial toxins of clinical relevance and the botulinum neurotoxin family in particular. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7qfq.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qfq.ent.gz | 196.4 KB | Display | PDB format |
PDBx/mmJSON format | 7qfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qfq_validation.pdf.gz | 717.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qfq_full_validation.pdf.gz | 730.9 KB | Display | |
Data in XML | 7qfq_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 7qfq_validation.cif.gz | 64.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/7qfq ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qfq | HTTPS FTP |
-Related structure data
Related structure data | 13947MC 7qfpC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 153021.922 Da / Num. of mol.: 1 / Mutation: E231Q, H234Y Source method: isolated from a genetically manipulated source Details: catalytically inactive variant of botulinum neurotoxin serotype B [E231Q/H234Y] Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10844 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Botulinum neurotoxin serotype B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.15 MDa / Experimental value: NO |
Source (natural) | Organism: Clostridium botulinum (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 / Details: 20 mM HEPES pH7.5, 50mM NaCl, 0.5mM TCEP |
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Pure protein, monodisperse by SEC |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6317 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2432309 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286802 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|