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- PDB-9phf: Vpb4Aa2 pore complex in C7 symmetry -

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Basic information

Entry
Database: PDB / ID: 9phf
TitleVpb4Aa2 pore complex in C7 symmetry
ComponentsVip4
KeywordsTOXIN / Vpb4 / Vip4 / bacterial toxin / pore-forming toxin / translocase / insecticidal
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 ...: / 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: 2.2 Å
AuthorsWirawan, R. / Spicer, B.A. / Lupton, C.J. / Venugopal, H. / Berry, C. / Dunstone, M.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Other privateGeorgina Sweet Award for Women in Quantitative Biomedical Science
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T019948/1, BB/S002774/1, BB/M009122/1 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for independent pore function of Vpb4 from Bacillus thuringiensis.
Authors: Raymond Wirawan / W David Jamieson / Hannah M Baird / Colin Berry / Christopher J Lupton / Hari Venugopal / Luis E Valentin-Alvarado / Hannah L Best / D Dafydd Jones / Lainey J Williamson / ...Authors: Raymond Wirawan / W David Jamieson / Hannah M Baird / Colin Berry / Christopher J Lupton / Hari Venugopal / Luis E Valentin-Alvarado / Hannah L Best / D Dafydd Jones / Lainey J Williamson / Husam Sabah Auhim / Oliver K Castell / Michelle A Dunstone / Bradley A Spicer /
Abstract: The Bacterial_Exotoxin_B family constitutes translocating pore-forming proteins that function as the binding (B) component in the binary AB Toxin mechanism. While the two-component system of the ...The Bacterial_Exotoxin_B family constitutes translocating pore-forming proteins that function as the binding (B) component in the binary AB Toxin mechanism. While the two-component system of the family is consistent among well-characterised members, the single-component Vpb4 subclass from entomopathogenic Bacillus thuringiensis challenges this dogma. Here, through single-particle cryo-electron microscopy, we elucidate the inserted pore structure of a Vpb4 member, Vpb4Aa2, at 2.2 Å resolution. The structure reveals distinguishing features from other family members: missing molecular bottleneck and neutrally charged β-barrel. Accordingly, preliminary electrophysiology studies show greater ion flux by Vpb4Aa2 compared to archetypal family member, PA. Through our findings, structure-guided database search allows identification of putative Vpb4-like proteins, which suggest a broader class of single-component proteins within the larger family. This provides mechanistic understanding of the differences between independent pores and translocating pores, with implications in the agricultural industry for screening and identification of future pest control candidates.
History
DepositionJul 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.1Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vip4
B: Vip4
C: Vip4
D: Vip4
E: Vip4
F: Vip4
G: Vip4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)588,48128
Polymers587,6397
Non-polymers84221
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Vip4


Mass: 83948.492 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: Natural variant of Vip4 (V9I0N3) from Bacillus thuringiensis strain V004.17
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: V004.17 / Gene: vip4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V9I0N3
#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: Heptameric pore complex of Vpb4Aa2 in LMNG/CHS detergent.
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: V004.17
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethane(HOCH2)3CNH21
2150 mMSodium chlorideNaCl1
30.01 mMLauryl Maltose Neopentyl GlycolC47H88O221
40.001 mMCholesteryl hemisuccinateC31H50O4-C4H11NO31
SpecimenConc.: 7.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: 3000 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149924 / Num. of class averages: 2 / Symmetry type: POINT

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