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- EMDB-71647: Vpb4Aa2 pore complex in C7 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-71647
TitleVpb4Aa2 pore complex in C7 symmetry
Map data
Sample
  • Complex: Heptameric pore complex of Vpb4Aa2 in LMNG/CHS detergent.
    • Protein or peptide: Vip4
  • Ligand: CALCIUM ION
KeywordsVpb4 / Vip4 / bacterial toxin / pore-forming toxin / translocase / insecticidal / TOXIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWirawan R / Spicer BA / Lupton CJ / Venugopal H / Berry C / Dunstone MA
Funding support United Kingdom, 2 items
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 WD / Baird HM / Berry C / Lupton CJ / Venugopal H / Valentin-Alvarado LE / Best HL / Jones DD / Wiliamson LJ / Al-Maslookhi HS / Castell OK / Dunstone MA / Spicer BA
History
DepositionJul 9, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71647.png

Downloads & links

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Map

FileDownload / File: emd_71647.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 328. Å		1.03 Å/pix.
x 320 pix.
= 328. Å		1.03 Å/pix.
x 320 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0058
Minimum - Maximum-0.022356167 - 0.06601908
Average (Standard dev.)-0.00015797724 (±0.00155352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71647_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_71647_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71647_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_71647_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 : Heptameric pore complex of Vpb4Aa2 in LMNG/CHS detergent.

EntireName: Heptameric pore complex of Vpb4Aa2 in LMNG/CHS detergent.
Components
  • Complex: Heptameric pore complex of Vpb4Aa2 in LMNG/CHS detergent.
    • Protein or peptide: Vip4
  • Ligand: CALCIUM ION

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Supramolecule #1: Heptameric pore complex of Vpb4Aa2 in LMNG/CHS detergent.

SupramoleculeName: Heptameric pore complex of Vpb4Aa2 in LMNG/CHS detergent.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: V004.17

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Macromolecule #1: Vip4

MacromoleculeName: Vip4 / type: protein_or_peptide / ID: 1
Details: Natural variant of Vip4 (V9I0N3) from Bacillus thuringiensis strain V004.17
Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: V004.17
Molecular weightTheoretical: 83.948492 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NMEDTDQDGI PDEWEEKGYT FKNQQIVKWD DSYLSQGYKK YLSNPYKART IADPYTDFEK VSGHMPAATK EDARDPLVAA YPAVGVGME NLLFSKNENV TEGSSGTMSK SVTDTNTNTN NVDLSAKLGW NDKGFGFEFT PKYSHTWTNS TAIQNSESES W SSQVGINS ...String:
NMEDTDQDGI PDEWEEKGYT FKNQQIVKWD DSYLSQGYKK YLSNPYKART IADPYTDFEK VSGHMPAATK EDARDPLVAA YPAVGVGME NLLFSKNENV TEGSSGTMSK SVTDTNTNTN NVDLSAKLGW NDKGFGFEFT PKYSHTWTNS TAIQNSESES W SSQVGINS AESAYLNANV RYYNAGTAPI YDLKPTTNFV LQNSGKSLAT ITAGPNQIGN SLGPGDTYPK VGQAPISLDK AN DAGTVKI PINKDYLNAL QSNSEALNLE TTQNKGQYGV LDATGQLITD SSKQWDPVRT NIDSVSGSLT LNLGSSKESL ERR VAAKND DDPEDKTPEI TIGEAIKKAF NAKEKDGRLY YVNSNGENVF LDESSINLIG DENTKKDIEQ QLEHMEDKKV YNAK WKRDM KITIHVPTSY YDFEKSGDSQ WHNTYQDNGG YTGEKTGRIN PRSNGYAIKD FTLKPYTSYT ARAYVKASSS ETDAV FYVD SDINSIGKGI KQNIKATGDK WKLVEMSFNT GSNPELFKKV GFKNQGNVQL QFDDVSVTEW KTEENLEKTH SMENWD VDP SKKYVKGGTF SHVPNSKIRY QWKINDNWEK IIPAPPVDNY GKRVMEKNFN FNDHVELYAV DEHNDYLKVK VAEHNKG DA ITEDVLKSSH QFSTWIKSKA PGGGSYTDGW YFERIPDGVL NCVTKYKVSI NGGKPVTRDR YNPDKNGRME VNLLEYNG G RGVKEGSRIE AWAILSNGKE AKVLDKKTS

UniProtKB: Vip4

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 21 / 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

Concentration7.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mM(HOCH2)3CNH2tris(hydroxymethyl)aminomethane
150.0 mMNaClSodium chloride
0.01 mMC47H88O22Lauryl Maltose Neopentyl Glycol
0.001 mMC31H50O4-C4H11NO3Cholesteryl hemisuccinate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 3.8000000000000003 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 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: OTHER / Details: 3D Initial Reference
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 149924
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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