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- EMDB-47974: VIP3Cb1 Protoxin Structure -

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Basic information

Entry
Database: EMDB / ID: EMD-47974
TitleVIP3Cb1 Protoxin Structure
Map dataSharpened EM map of VIP3Cb1 protoxin
Sample
  • Complex: VIP3Cb1 Protoxin Tetramer - Disable Toxin Variant
    • Protein or peptide: VIP3Cb1 Protoxin Structure - Disable Toxin Variant
KeywordsTetramer / Protoxin / Lepidopteran / TOXIN
Biological speciesPaenibacillus popilliae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsRau MJ / Rydel T / Zheng M / White T
Funding support1 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47974.png

Downloads & links

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Map

FileDownload / File: emd_47974.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened EM map of VIP3Cb1 protoxin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.92 Å		1.08 Å/pix.
x 320 pix.
= 345.92 Å		1.08 Å/pix.
x 320 pix.
= 345.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.081 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.6021171 - 3.5087776
Average (Standard dev.)-0.00025475628 (±0.075707264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened focused refinement map of VIP3Cb1 protoxin chain A

Fileemd_47974_additional_1.map
AnnotationSharpened focused refinement map of VIP3Cb1 protoxin chain A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened focused refinement map of VIP3Cb1 protoxin chain B

Fileemd_47974_additional_2.map
AnnotationSharpened focused refinement map of VIP3Cb1 protoxin chain B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map B of VIP3Cb1 protoxin

Fileemd_47974_half_map_1.map
AnnotationUnsharpened half map B of VIP3Cb1 protoxin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map A of VIP3Cb1 protoxin

Fileemd_47974_half_map_2.map
AnnotationUnsharpened half map A of VIP3Cb1 protoxin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VIP3Cb1 Protoxin Tetramer - Disable Toxin Variant

EntireName: VIP3Cb1 Protoxin Tetramer - Disable Toxin Variant
Components
  • Complex: VIP3Cb1 Protoxin Tetramer - Disable Toxin Variant
    • Protein or peptide: VIP3Cb1 Protoxin Structure - Disable Toxin Variant

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Supramolecule #1: VIP3Cb1 Protoxin Tetramer - Disable Toxin Variant

SupramoleculeName: VIP3Cb1 Protoxin Tetramer - Disable Toxin Variant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Paenibacillus popilliae (bacteria)

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Macromolecule #1: VIP3Cb1 Protoxin Structure - Disable Toxin Variant

MacromoleculeName: VIP3Cb1 Protoxin Structure - Disable Toxin Variant / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus popilliae (bacteria)
Molecular weightTheoretical: 92.486547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHHHH HGTETVRFQS KQNNNFSVRA LPSFIDVFNG IYGFATGIQD IFNMIFGTDT GDLTLEEVLK NQELLYDISG KLEGISGDL SEIIAQGNLN TELAKELLKI ANEQNNVLTD VNNKLNAINS MLHIYLPKIT NMLSDVMKQN YALSLQIEYL S KQLQEISD ...String:
MHHHHHHHHH HGTETVRFQS KQNNNFSVRA LPSFIDVFNG IYGFATGIQD IFNMIFGTDT GDLTLEEVLK NQELLYDISG KLEGISGDL SEIIAQGNLN TELAKELLKI ANEQNNVLTD VNNKLNAINS MLHIYLPKIT NMLSDVMKQN YALSLQIEYL S KQLQEISD KLDVINLNVL INCTCTEITP AYQRIKYVNE KFDELTLATE KTLRAKQGSE DIIANDTLEN LTELTELAKS VT KNDMDSF EFYLHTFHDV LIGNNLFGRS ALKTAAELIT KDEIKTSGSE IGKVYSFLIV LTCLQAKAFL TLTACRKLLG LSD IDYTNI LNQHLNDEKN VFRDNILPTL SNKFSNPNYV KTIGSDNYAK VILEAEPGYA LVGFEIINDR IPVLKAYKAK LKQN YQVDH QSLSEIVYLD IDKLFCPKNS EQKYYTKSLT FPDGYVITKI TFEKKLNNLR YEATANFYDP STGDIDLNEK QVEST FLQA DYISINVSDD DGVYMPLGVI SETFLSPINS FELEVDEKSK ILTLTCKSYL REYLLESDLI NKETSLIAPP NVFISN IVE NWNIEADNLE PWVANNKNAY VDSTGGIEGS KALFTQGDGE FSQFIGDKLK PNTDYIIQYT VKGKPAIYLK NKNTGYT MY EDTNGSSEEF QTIAVNYTSE TDPSQTHLVF KSQSGYEAWG DNFIILECKA FETPEGPELI KFDDWISFGT TYIRDDVL T IDPSRGGYFR QSLKLDSYST YNLSFSFSGL WAKVIIKNSH GVVLFEKVSQ QSSYVDISES FTTTSNKEGF FIELTGDSR GGFGSFRDFS MKEKFE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8
Details: 50 mM Tris-HCl pH8.0, 500 mM NaCl, 5 mM MgCl2, 2mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4547 / Average exposure time: 13.29 sec. / Average electron dose: 57.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2763759
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1557854
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9efi:
VIP3Cb1 Protoxin Structure

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