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- PDB-9vek: Structural basis for the assembly and translocation of the Vip1-V... -

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Basic information

Entry
Database: PDB / ID: 9vek
TitleStructural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis
ComponentsVip1
KeywordsTOXIN / binary toxin / biopesticide
Function / homology
Function and homology information


protein homooligomerization / extracellular region
Similarity search - Function
PA14/GLEYA domain / PA14 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/GLEYA domain / PA14 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsChen, P. / Zhao, T.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vip1
B: Vip1
C: Vip1
D: Vip1
E: Vip1
F: Vip1
G: Vip1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)509,42328
Polymers508,5817
Non-polymers84221
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
Vip1


Mass: 72654.477 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: vip1 / Production host: Bacillus thuringiensis (bacteria) / References: UniProt: A0A075BFL2
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Vip1Ad1 heptamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Bacillus thuringiensis (bacteria)
Source (recombinant)Organism: Bacillus thuringiensis (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.16_3549model refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43696 / Symmetry type: POINT
RefinementHighest resolution: 3.31 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00229834
ELECTRON MICROSCOPYf_angle_d0.45540495
ELECTRON MICROSCOPYf_dihedral_angle_d4.0534032
ELECTRON MICROSCOPYf_chiral_restr0.0444550
ELECTRON MICROSCOPYf_plane_restr0.0035257

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