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- PDB-9efi: VIP3Cb1 Protoxin Structure -

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Basic information

Entry
Database: PDB / ID: 9efi
TitleVIP3Cb1 Protoxin Structure
ComponentsVIP3Cb1 Protoxin Structure - Disable Toxin Variant
KeywordsTOXIN / Tetramer / Protoxin / Lepidopteran
Biological speciesPaenibacillus popilliae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsRau, M.J. / Rydel, T. / Zheng, M. / White, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl Environ Microbiol / Year: 2025
Title: Vip3C proteins from spp. for controlling lepidopteran crop pests.
Authors: Todd Ciche / William Moar / Aqeel Ahmad / David Bowen / Catherine Chay / Arlene Howe / Uma Kesanapalli / Jennifer Lutke / Gregory Bean / Jason Milligan / Michael Pleau / Yong Yin / Waseem ...Authors: Todd Ciche / William Moar / Aqeel Ahmad / David Bowen / Catherine Chay / Arlene Howe / Uma Kesanapalli / Jennifer Lutke / Gregory Bean / Jason Milligan / Michael Pleau / Yong Yin / Waseem Akbar / Marty Heppler / Cara Griffith / Kimberly Morrell / Katherine Dunkmann / Heather Anderson / Jeffrey Ahrens / Pacifica Sommers / E Sethe Burgie / Fred Zinnel / Meiying Zheng / James Fitzpatrick / Michael Rau / Timothy Rydel / Tommi White / David Kerns / James Roberts /
Abstract: New proteins are needed to control insects not controlled with (Bt) crops, and those evolving resistance to Bt crops. These proteins are increasingly being reported from non-Bt organisms to control ...New proteins are needed to control insects not controlled with (Bt) crops, and those evolving resistance to Bt crops. These proteins are increasingly being reported from non-Bt organisms to control Bt-resistant insects. However, these proteins mostly control the corn rootworm, spp. (Coleoptera), whereas most Bt-resistant insects are lepidopteran. We hypothesized that diversifying our search for proteins into non-Bt organisms, such as those related to used to control Japanese beetle , could yield proteins with new insecticidal activities against Lepidoptera. Here, we identified Vip3Cb1 and Vip3Cc1 with broad lepidopteran activity, the first Vip3 proteins discovered from strains in the containing clade. Vip3Cb1 protected plants against cotton bollworm, and tobacco budworm and fall armyworm, , and Southwestern corn borer, , in cotton and maize, respectively, like commercial Vip3Aa. Distinct from Vip3Aa, Vip3Cb1 also protected maize against European corn borer, , the primary maize pest in the United States, with recent reports of resistance to Bt proteins. Consistent with previous reports, insects resistant to Vip3Aa were cross-resistant to Vip3Cb1. Cryo-electron microscopy demonstrated that Vip3Cb1 formed a pore-shaped tetramer upon proteolytic activation, in agreement with the pore-forming mechanism of action of Vip3Aa. Thus, diversifying the search beyond Bt has led to the discovery of the first Vip3 proteins from spp. with different activity spectra from Vip3Aa, providing additional tools to control pests, including those currently resistant to Bt Cry proteins.IMPORTANCENew insecticidal proteins are needed for controlling insect pests that can devastate crop yield if left uncontrolled. Diversifying our search for new insecticidal proteins in spp. resulted in the discovery of Vip3Cb1 and Vip3Cc1 insecticidal proteins active against lepidopteran crop pests. Structure and cross-resistance studies indicate overlap in the mechanism of action between Vip3Cb1 and commercial Vip3Aa. However, new activities, such as controlling European corn borer, make these proteins important new tools in the insect control toolbox.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VIP3Cb1 Protoxin Structure - Disable Toxin Variant
B: VIP3Cb1 Protoxin Structure - Disable Toxin Variant
C: VIP3Cb1 Protoxin Structure - Disable Toxin Variant
D: VIP3Cb1 Protoxin Structure - Disable Toxin Variant


Theoretical massNumber of molelcules
Total (without water)369,9464
Polymers369,9464
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
VIP3Cb1 Protoxin Structure - Disable Toxin Variant


Mass: 92486.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus popilliae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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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: VIP3Cb1 Protoxin Tetramer - Disable Toxin Variant / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Paenibacillus popilliae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Details: 50 mM Tris-HCl pH8.0, 500 mM NaCl, 5 mM MgCl2, 2mM DTT
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 13.29 sec. / Electron dose: 57.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4547

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2763759
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1557854 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00225174
ELECTRON MICROSCOPYf_angle_d0.40734100
ELECTRON MICROSCOPYf_dihedral_angle_d9.9799228
ELECTRON MICROSCOPYf_chiral_restr0.0393898
ELECTRON MICROSCOPYf_plane_restr0.0034372

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