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- PDB-6yrf: Vip3Bc1 tetramer -

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Basic information

Entry
Database: PDB / ID: 6yrf
TitleVip3Bc1 tetramer
ComponentsVegetative insecticidal protein
KeywordsTOXIN / Vip3 / Bt toxin
Function / homologyVegetative insecticide protein 3 / Vegetative insecticide protein 3A N terminal / Vegetative insecticidal protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsThompson, 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.
CitationJournal: 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
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Vegetative insecticidal protein
B: Vegetative insecticidal protein
C: Vegetative insecticidal protein
D: Vegetative insecticidal protein


Theoretical massNumber of molelcules
Total (without water)365,1494
Polymers365,1494
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16340 Å2
ΔGint-95 kcal/mol
Surface area126330 Å2
MethodPISA

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Components

#1: Protein
Vegetative insecticidal 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric assembly of Vip3Bc1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus thuringiensis (bacteria)
Source (recombinant)Organism: Pseudomonas fluorescens (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage 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

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1414999 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 149.98 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625268
ELECTRON MICROSCOPYf_angle_d0.72534176
ELECTRON MICROSCOPYf_dihedral_angle_d11.0683316
ELECTRON MICROSCOPYf_chiral_restr0.0463884
ELECTRON MICROSCOPYf_plane_restr0.0044404

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