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- EMDB-65007: Structural basis for the assembly and translocation of the Vip1-V... -

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Basic information

Entry
Database: EMDB / ID: EMD-65007
TitleStructural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis
Map data
Sample
  • Complex: Vip2-bound Vip1-pore heptamer complex
    • Protein or peptide: Vip1
    • Protein or peptide: Vip2
  • Ligand: CALCIUM ION
Keywordsbinary toxin / biopesticide / TOXIN
Function / homology
Function and homology information


protein homooligomerization / extracellular region
Similarity search - Function
Binary exotoxin A, clostridial type / PA14/GLEYA domain / PA14 domain profile. / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 ...Binary exotoxin A, clostridial type / PA14/GLEYA domain / PA14 domain profile. / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 domain / PA14 / PA14 domain
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsChen P / Zhao T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for the assembly and translocation of the Vip1-Vip2 insecticidal toxin from Bacillus thuringiensis.
Authors: Ting Zhao / Zeyu Wang / Jing Ren / Xianle Han / Linpeng Li / Zheng Liu / Jie Zhang / Peng Chen /
Abstract: Insecticidal toxins from Bacillus thuringiensis (Bt) have been extensively and successfully used in genetically engineered crops for decades but continue to face challenges from the adaptive ...Insecticidal toxins from Bacillus thuringiensis (Bt) have been extensively and successfully used in genetically engineered crops for decades but continue to face challenges from the adaptive resistance in the insect population. The Bt binary toxin Vip1Ad1(Vip1) and Vip2Ag1(Vip2), a promising next-generation candidate gene combination for transgenic crops, have demonstrated high efficacy against the destructive coleopteran pest white grubs, however, their mode of action remains largely elusive. In this study, we report cryo-EM structures of the heptameric Vip1-pore and Vip2-bound Vip1-pore complex, capturing a series of putative assembly-related intermediates that suggest a binary toxin assembly and translocation pathway. Together with structure-guided mutagenesis, these data provide insights into a sequential assembly of binary complex and a sequence-independent translocation mechanism. Proof-of-principle experiments showed successful delivery of a desired protein cargo into host cells based on the mini-Vip2-Vip1 pore system, paving the way for developing much needed extracellular pesticidal protein delivery platforms. These findings not only clarify the assembly and translocation mechanism of the binary insecticidal toxin pair but also offer an excellent alternative model to investigate human-pathogenic pore-forming toxins because of its similarity and biosafety.
History
DepositionJun 9, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65007.png

Downloads & links

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Map

FileDownload / File: emd_65007.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 430.08 Å		0.84 Å/pix.
x 512 pix.
= 430.08 Å		0.84 Å/pix.
x 512 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.33814716 - 0.7276105
Average (Standard dev.)0.00004885584 (±0.013715633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65007_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65007_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vip2-bound Vip1-pore heptamer complex

EntireName: Vip2-bound Vip1-pore heptamer complex
Components
  • Complex: Vip2-bound Vip1-pore heptamer complex
    • Protein or peptide: Vip1
    • Protein or peptide: Vip2
  • Ligand: CALCIUM ION

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Supramolecule #1: Vip2-bound Vip1-pore heptamer complex

SupramoleculeName: Vip2-bound Vip1-pore heptamer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus thuringiensis (bacteria)

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Macromolecule #1: Vip1

MacromoleculeName: Vip1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis (bacteria)
Molecular weightTheoretical: 72.654477 KDa
Recombinant expressionOrganism: Bacillus thuringiensis (bacteria)
SequenceString: DEDTDTDGDS IPDLWEENGY TIQNRIAVKW DDSLASKGYT KFVSNPLDSH TVGDPYTDYE KAARDLDMSN AKETFNPLVA AFPSVNVNM EKVILSPNKN LSNSVESHSS TNWSYTNTVG ASVEAGFGPK GLSFGVSASY QHSETVAQEW GTSKGNTSQF N TASAGYLN ...String:
DEDTDTDGDS IPDLWEENGY TIQNRIAVKW DDSLASKGYT KFVSNPLDSH TVGDPYTDYE KAARDLDMSN AKETFNPLVA AFPSVNVNM EKVILSPNKN LSNSVESHSS TNWSYTNTVG ASVEAGFGPK GLSFGVSASY QHSETVAQEW GTSKGNTSQF N TASAGYLN ANVRYNNVGT GAIYEVKPTT SFVLDKNTIA TITAKSNSTA LNISPGESYP KKGQNGIAIT SMDDFNSHPI TL NKQQVDQ LLNNKPMMLE TNQTDGVYKI KDTHGNIVTG GEWNGVTQQI KAKTASIIVD NGERVSEKRV AAKDYDYPED KTP SLTLKD ALKLSYPDEI KETDGLLYYN DKPIYESSVM TYLDENTAKE VKKQLNDTTG KFKDVNHLYD VKLTPRMNFT IKMS SLYDG AEGGSSSKPI GTWYNTSYVN GGNTGKKQFQ SANSNAYVAL SSEAKKKLNQ SVNYYLSMYM KADSTTEPTV EVVGA KSTI TSKKVKLNNQ GYQRVDILVK NSERNLIDKI YIKGNGKTNV YWDDVTISEI SAINPASLSD IEIQEIFKDS TIQYGN PSF AIDFITFKNI KPLQNYIKQY EIYQKIVGID LGTGKEVITE NTFNTEGDLK EDGSVKIDVR KNGFGFITFK GSNLKIQ AI ANDGRKIEVF NKIF

UniProtKB: Vip1

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Macromolecule #2: Vip2

MacromoleculeName: Vip2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis (bacteria)
Molecular weightTheoretical: 45.389523 KDa
Recombinant expressionOrganism: Bacillus thuringiensis (bacteria)
SequenceString: KAEDFKEDKE KAKEWGKEKE KEWKLTATEK GKMNDFLNDK NKIKTNYKEI TFSMAGSFED EMKNLKEIDK MFDKANLSSS IITYKNVEP ATIGFNKSLI EGNTINSDAL AQFKEQFLDR DMKFDSYLDT HLTAQQVSSK ERVIMKVTVP SGKGSTTPTK A GVILNNNE ...String:
KAEDFKEDKE KAKEWGKEKE KEWKLTATEK GKMNDFLNDK NKIKTNYKEI TFSMAGSFED EMKNLKEIDK MFDKANLSSS IITYKNVEP ATIGFNKSLI EGNTINSDAL AQFKEQFLDR DMKFDSYLDT HLTAQQVSSK ERVIMKVTVP SGKGSTTPTK A GVILNNNE YKMLIDNGYV LHVDKVSKVV KKGFECVQVE GILKKSLDFK NDINAESHSW GMKNYEGWAK NLTDSQREAL DG YARQDYK EINDYLRNQG GSGNEKLDAQ IKNISEALGK KPIPENITVY RWCGMPEFGY QISDPLPSLK DFEEKFLNTI KED KGYMST SLSSERLAAF GSRKIILRLQ VPKGSTGAYL SAIGGFASEK EILLDKDSKY HIDKVTEVVI KGVKRYVIDA TLLT

UniProtKB: Vip2

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 107143
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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