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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: Wirawan, R. / Jamieson, W.D. / Baird, H.M. / Berry, C. / Lupton, C.J. / Venugopal, H. / Valentin-Alvarado, L.E. / Best, H.L. / Jones, D.D. / Wiliamson, L.J. / Al-Maslookhi, H.S. / Castell, O. ...Authors: Wirawan, R. / Jamieson, W.D. / Baird, H.M. / Berry, C. / Lupton, C.J. / Venugopal, H. / Valentin-Alvarado, L.E. / Best, H.L. / Jones, D.D. / Wiliamson, L.J. / Al-Maslookhi, H.S. / Castell, O.K. / Dunstone, M.A. / Spicer, B.A.
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

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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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