+Open data
-Basic information
Entry | Database: PDB / ID: 7ntx | |||||||||
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Title | Vip3Bc1 tetramer in processed, activated state | |||||||||
Components | Vegetative insecticidal protein | |||||||||
Keywords | TOXIN / Vip3 / Bt toxin | |||||||||
Function / homology | Vegetative insecticide protein 3 / Vegetative insecticide protein 3A N terminal / Vegetative insecticidal protein Function and homology information | |||||||||
Biological species | Bacillus thuringiensis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.75 Å | |||||||||
Authors | Thompson, R.F. / Byrne, M.J. / Iadanza, M.I. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Cryo-EM structures of an insecticidal Bt toxin reveal its mechanism of action on the membrane. Authors: Matthew J Byrne / Matthew G Iadanza / Marcos Arribas Perez / Daniel P Maskell / Rachel M George / Emma L Hesketh / Paul A Beales / Marc D Zack / Colin Berry / Rebecca F Thompson / Abstract: Insect pests are a major cause of crop losses worldwide, with an estimated economic cost of $470 billion annually. Biotechnological tools have been introduced to control such insects without the need ...Insect pests are a major cause of crop losses worldwide, with an estimated economic cost of $470 billion annually. Biotechnological tools have been introduced to control such insects without the need for chemical pesticides; for instance, the development of transgenic plants harbouring genes encoding insecticidal proteins. The Vip3 (vegetative insecticidal protein 3) family proteins from Bacillus thuringiensis convey toxicity to species within the Lepidoptera, and have wide potential applications in commercial agriculture. Vip3 proteins are proposed to exert their insecticidal activity through pore formation, though to date there is no mechanistic description of how this occurs on the membrane. Here we present cryo-EM structures of a Vip3 family toxin in both inactive and activated forms in conjunction with structural and functional data on toxin-membrane interactions. Together these data demonstrate that activated Vip3Bc1 complex is able to insert into membranes in a highly efficient manner, indicating that receptor binding is the likely driver of Vip3 specificity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ntx.cif.gz | 456.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ntx.ent.gz | 378.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ntx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ntx_validation.pdf.gz | 874.4 KB | Display | wwPDB validaton report |
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Full document | 7ntx_full_validation.pdf.gz | 986.5 KB | Display | |
Data in XML | 7ntx_validation.xml.gz | 92.4 KB | Display | |
Data in CIF | 7ntx_validation.cif.gz | 135.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/7ntx ftp://data.pdbj.org/pub/pdb/validation_reports/nt/7ntx | HTTPS FTP |
-Related structure data
Related structure data | 10889MC 6yrfC 6yrgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 91287.148 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: vip3Bc1 / Production host: Pseudomonas fluorescens (bacteria) / References: UniProt: A0A290WPI2 |
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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: activated form of Vip3bc1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
Source (recombinant) | Organism: Pseudomonas fluorescens (bacteria) |
Buffer solution | pH: 8 / Details: 25mM TrisHCl pH 8 150mM NaCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / 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 |
Image recording | Electron dose: 70.8 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158763 / Symmetry type: POINT |