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- EMDB-49339: The structure of BoNT/A in complex with a neutralizing antibody 2G11 -

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Basic information

Entry
Database: EMDB / ID: EMD-49339
TitleThe structure of BoNT/A in complex with a neutralizing antibody 2G11
Map data
Sample
  • Complex: BoNT-antibody
    • Protein or peptide: Botulinum neurotoxin type A
    • Protein or peptide: Heavy Chain
    • Protein or peptide: Light Chain
KeywordsBoNT / antibody / IMMUNE SYSTEM-TOXIN complex
Biological speciesClostridium botulinum (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsChen B / Jin R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 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
DepositionFeb 20, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49339.png

Downloads & links

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Map

FileDownload / File: emd_49339.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 317.414 Å		0.83 Å/pix.
x 384 pix.
= 317.414 Å		0.83 Å/pix.
x 384 pix.
= 317.414 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8266 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.3110534 - 1.8864163
Average (Standard dev.)0.00059903314 (±0.031017603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.4144 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49339_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_49339_half_map_2.map
Projections & Slices
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Sample components

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Entire : BoNT-antibody

EntireName: BoNT-antibody
Components
  • Complex: BoNT-antibody
    • Protein or peptide: Botulinum neurotoxin type A
    • Protein or peptide: Heavy Chain
    • Protein or peptide: Light Chain

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Supramolecule #1: BoNT-antibody

SupramoleculeName: BoNT-antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Botulinum neurotoxin type A

MacromoleculeName: Botulinum neurotoxin type A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 149.862266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMPFVN KQFNYKDPVN GVDIAYIKIP NAGQMQPVKA FKIHNKIWVI PERDTFTNPE EGDLNPPPEA KQVPVSYYDS TYLSTDNEK DNYLKGVTKL FERIYSTDLG RMLLTSIVRG IPFWGGSTID TELKVIDTNC INVIQPDGSY RSEELNLVII G PSADIIQF ...String:
GPLGSMPFVN KQFNYKDPVN GVDIAYIKIP NAGQMQPVKA FKIHNKIWVI PERDTFTNPE EGDLNPPPEA KQVPVSYYDS TYLSTDNEK DNYLKGVTKL FERIYSTDLG RMLLTSIVRG IPFWGGSTID TELKVIDTNC INVIQPDGSY RSEELNLVII G PSADIIQF ECKSFGHEVL NLTRNGYGST QYIRFSPDFT FGFEESLEVD TNPLLGAGKF ATDPAVTLAH ELIHAGHRLY GI AINPNRV FKVNTNAYYE MSGLEVSFEE LRTFGGHDAK FIDSLQENEF RLYYYNKFKD IASTLNKAKS IVGTTASLQY MKN VFKEKY LLSEDTSGKF SVDKLKFDKL YKMLTEIYTE DNFVKFFKVL NAKTFLNFDK AVFKINIVPK VNYTIYDGFN LRNT NLAAN FNGQNTEINN MNFTKLKNFT GLFEFYKLLC VRGIITSKTK SLDKGYNKAL NDLCIKVNNW DLFFSPSEDN FTNDL NKGE EITSDTNIEA AEENISLDLI QQYYLTFNFD NEPENISIEN LSSDIIGQLE LMPNIERFPN GKKYELDKYT MFHYLR AQE FEHGKSRIAL TNSVNEALLN PSRVYTFFSS DYVKKVNKAT EAAMFLGWVE QLVYDFTDET SEVSTTDKIA DITIIIP YI GPALNIGNML YKDDFVGALI FSGAVILLEF IPEIAIPVLG TFALVSYIAN KVLTVQTIDN ALSKRNEKWD EVYKYIVT N WLAKVNTQID LIRKKMKEAL ENQAEATKAI INYQYNQYTE EEKNNINFNI DDLSSKLNES INKAMININK FLNQCSVSY LMNSMIPYGV KRLEDFDASL KDALLKYIYD NRGTLIGQVD RLKDKVNNTL STDIPFQLSK YVDNQRLLST FTEYIKNIIN TSILNLRYE SNHLIDLSRY ASKINIGSKV NFDPIDKNQI QLFNLESSKI EVILKNAIVY NSMYENFSTS FWIRIPKYFN S ISLNNEYT IINCMENNSG WKVSLNYGEI IWTLQDTQEI KQRVVFKYSQ MINISDYINR WIFVTITNNR LNNSKIYING RL IDQKPIS NLGNIHASNN IMFKLDGCRD THRYIWIKYF NLFDKELNEK EIKDLYDNQS NSGILKDFWG DYLQYDKPYY MLN LYDPNK YVDVNNVGIR GYMYLKGPRG SVMTTNIYLN SSLYRGAKFI IKKYASGNKD NIVRNNDRVY INVVVKNKEY RLAT NASQA GVEKILSALE IPDVGNLSQV VVMKSKNDQG ITNKCKMNLQ DNNGNDIGFI GFHQFNNIAK LVASNWYNRQ IERSS RTLG CSWEFIPVDD GWGERPL

UniProtKB: Botulinum neurotoxin type A

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Macromolecule #2: Heavy Chain

MacromoleculeName: Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.483307 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQQSGGG LVQPGGSLRL SCAASGFTFS NYAMTWVRQA PGKGLEWVSS ISVGGSDTYY ADSVKGRFTV SRDNSKNTLL LQMNSLRAE DTAVYYCAKV RTKYCSSLSC FAGFDSWGQG TRVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLQQSGGG LVQPGGSLRL SCAASGFTFS NYAMTWVRQA PGKGLEWVSS ISVGGSDTYY ADSVKGRFTV SRDNSKNTLL LQMNSLRAE DTAVYYCAKV RTKYCSSLSC FAGFDSWGQG TRVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKK

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Macromolecule #3: Light Chain

MacromoleculeName: Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.414908 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DVVMTQSPSS LSASVGDRVT ITCRASQSIS SYLHWYQQKP GKAPTLLISD ASSSQSGVPS RFSGSRFGTD FTLTISSLQP EDFATYYCQ QSYSTRALTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DVVMTQSPSS LSASVGDRVT ITCRASQSIS SYLHWYQQKP GKAPTLLISD ASSSQSGVPS RFSGSRFGTD FTLTISSLQP EDFATYYCQ QSYSTRALTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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

BufferpH: 7.5
VitrificationCryogen name: PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 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: PDB ENTRY
PDB model - PDB ID:

3bta

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 730074
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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