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- EMDB-46410: CryoEM structure of BoNT/E-LCHn domain at pH5 -

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Basic information

Entry
Database: EMDB / ID: EMD-46410
TitleCryoEM structure of BoNT/E-LCHn domain at pH5
Map data
Sample
  • Complex: BoNT/Ei
    • Protein or peptide: Bont/E
KeywordsBotulinum neurotoxin / TOXIN
Function / homology
Function and homology information


host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / transmembrane protein transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium botulinum E1 str. 'BoNT E Beluga' (bacteria) / Clostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGao L
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI139087 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI158503 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI163178 United States
CitationJournal: Nat Commun / Year: 2026
Title: A belt-buckle checkpoint regulates the onset of botulinum neurotoxin intoxication.
Authors: Baohua Chen / Linfeng Gao / Melvin Bönninger / Ting Huang / Nadja Krez / Weihua Wen / Mark Bowen / Jianlong Lou / James D Marks / Andreas Rummel / Rongsheng Jin /
Abstract: Fast-acting botulinum neurotoxins (BoNTs) are highly desirable for both medical and aesthetic indications, but the underlying mechanism for the differing onset of BoNTs' action remains unknown. Here, ...Fast-acting botulinum neurotoxins (BoNTs) are highly desirable for both medical and aesthetic indications, but the underlying mechanism for the differing onset of BoNTs' action remains unknown. Here, we demonstrate that the "belt" of BoNTs, a largely unstructured loop wrapping around their catalytic light chain (LC), is key to onset of intoxication. The more flexible BoNT/E belt promotes quicker LC translocation into the neuronal cytosol, leading to faster onset of action compared to BoNT/A. Furthermore, we discover a "belt-buckle" checkpoint that regulates this process. By loosening the BoNT/A belt-buckle via protein engineering, we enhance its sensitivity to acidic pH, leading to an accelerated onset of action. Conversely, locking the belt-buckle with an antibody neutralizes BoNT/A. Our findings open avenues for developing fast-acting BoNTs and effective countermeasures.
History
DepositionAug 5, 2024-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46410.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 320 pix.
= 252.16 Å		0.79 Å/pix.
x 320 pix.
= 252.16 Å		0.79 Å/pix.
x 320 pix.
= 252.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.942313 - 1.349971
Average (Standard dev.)-0.00007082853 (±0.02424436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 252.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46410_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46410_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 : BoNT/Ei

EntireName: BoNT/Ei
Components
  • Complex: BoNT/Ei
    • Protein or peptide: Bont/E

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Supramolecule #1: BoNT/Ei

SupramoleculeName: BoNT/Ei / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum E1 str. 'BoNT E Beluga' (bacteria)
Molecular weightTheoretical: 143 KDa

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Macromolecule #1: Bont/E

MacromoleculeName: Bont/E / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 94.450055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPKINSFNYN DPVNDRTILY IKPGGCQEFY KSFNIMKNIW IIPERNVIGT TPQDFHPPTS LKNGDSSYYD PNYLQSDEEK DRFLKIVTK IFNRINNNLS GGILLEELSK ANPYLGNDNT PDNQFHIGDA SAVEIKFSNG SQDILLPNVI IMGAEPDLFE T NSSNISLR ...String:
MPKINSFNYN DPVNDRTILY IKPGGCQEFY KSFNIMKNIW IIPERNVIGT TPQDFHPPTS LKNGDSSYYD PNYLQSDEEK DRFLKIVTK IFNRINNNLS GGILLEELSK ANPYLGNDNT PDNQFHIGDA SAVEIKFSNG SQDILLPNVI IMGAEPDLFE T NSSNISLR NNYMPSNHGF GSIAIVTFSP EYSFRFNDNS MNEFIQDPAL TLMAALIASL HGLYGAKGIT TKYTITQKQN PL ITNIRGT NIEEFLTFGG TDLNIITSAQ SNDIYTNLLA DYKKIASKLS KVQVSNPLLN PYKDVFEAKY GLDKDASGIY SVN INKFND IFKKLYSFTE FDLATKFQVK CRQTYIGQYK YFKLSNLLND SIYNISEGYN INNLKVNFRG QNANLNPRII TPIT GRGLV KKIIRFCKNI VSVKGIRKSI CIEINNGELF FVASENSYND DNINTPKEID DTVTSNNNYE NDLDQVILNF NSESA PGLS DEKLNLTIQN DAYIPKYDSN GTSDIEQHDV NELNVFFYLD AQKVPEGENN VNLTSSIDTA LLEQPKIYTF FSSEFI NNV NKPVQAALFV SWIQQVLVDF TTEANQKSTV DKIADISIVV PYIGLALNIG NEAQKGNFKD ALELLGAGIL LEFEPEL LI PTILVFTIKS FLGSSDNKNK VIKAINNALK ERDEKWKEVY SFIVSNWMTK INTQFNKRKE QMYQALQNQV NAIKTIIE S KYNSYTLEEK NELTNKYDIK QIENELNQKV SIAMNNIDRF LTESSISYLM KLINEVKINK LREYDENVKT YLLNYIIQH GSILGESQQE LNSMVTDTLN NSIPFKLSSY T

UniProtKB: Bont/E

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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

Concentration0.5 mg/mL
BufferpH: 5
Component:
ConcentrationFormulaName
0.05 MNa-AcetateNa-Acetate
0.1 MNaClNaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.7000000000000001 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 266682
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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