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- PDB-7ntx: Vip3Bc1 tetramer in processed, activated state -

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Basic information

Entry
Database: PDB / ID: 7ntx
TitleVip3Bc1 tetramer in processed, activated state
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: 4.75 Å
AuthorsThompson, R.F. / Byrne, M.J. / Iadanza, M.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012573/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
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
DepositionMar 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 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
Revision 1.2Jul 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15160 Å2
ΔGint-84 kcal/mol
Surface area110540 Å2

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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: activated form 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: 8 / Details: 25mM TrisHCl pH 8 150mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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 FIELD
Image recordingElectron dose: 70.8 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158763 / Symmetry type: POINT

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