+Open data
-Basic information
Entry | Database: PDB / ID: 6yrf | ||||||
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Title | Vip3Bc1 tetramer | ||||||
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: 3.9 Å | ||||||
Authors | Thompson, R.F. / Byrne, M.J. / Iadanza, M.I. / Arribas Perez, M. / Maskell, D.P. / George, R.M. / Hesketh, E.L. / Beales, P.A. / Zack, M.D. / Berry, C. | ||||||
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 | 6yrf.cif.gz | 533 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yrf.ent.gz | 445.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yrf_validation.pdf.gz | 878.1 KB | Display | wwPDB validaton report |
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Full document | 6yrf_full_validation.pdf.gz | 986.4 KB | Display | |
Data in XML | 6yrf_validation.xml.gz | 98.4 KB | Display | |
Data in CIF | 6yrf_validation.cif.gz | 147 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yrf ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yrf | HTTPS FTP |
-Related structure data
Related structure data | 10888MC 6yrgC 7ntxC 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: Tetrameric assembly 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: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % |
-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 | Average exposure time: 1.5 sec. / Electron dose: 76.7 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1414999 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 149.98 Å2 | ||||||||||||||||||||||||
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