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- EMDB-50151: Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-50151
TitleCryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5
Map data
Sample
  • Complex: Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5
    • Protein or peptide: Synaptic vesicle glycoprotein 2B
    • Protein or peptide: Botulinum neurotoxin A
Keywordstransporter / botulinum neurotoxin / synaptic vesicle glycoprotein / MEMBRANE PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host exocytosis / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / regulation of presynaptic cytosolic calcium ion concentration / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle ...symbiont-mediated suppression of host exocytosis / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / regulation of presynaptic cytosolic calcium ion concentration / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / neurotransmitter transport / regulation of synaptic vesicle exocytosis / protein transmembrane transporter activity / transmembrane transporter activity / acrosomal vesicle / metalloendopeptidase activity / synaptic vesicle / synaptic vesicle membrane / toxin activity / chemical synaptic transmission / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane / plasma membrane
Similarity search - Function
: / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal ...: / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / 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 / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin type A / Synaptic vesicle glycoprotein 2B
Similarity search - Component
Biological speciesClostridium botulinum (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.41 Å
AuthorsKhanppnavar B / Leka O / Korkhov V / Kammerer R
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_212253 Switzerland
Swiss National Science Foundation198545 Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure of the botulinum neurotoxin A/SV2B complex and its implications for translocation.
Authors: Basavraj Khanppnavar / Oneda Leka / Sushant K Pal / Volodymyr M Korkhov / Richard A Kammerer /
Abstract: Botulinum neurotoxin A1 (BoNT/A1) belongs to the most potent toxins and is used as a major therapeutic agent. Neurotoxin conformation is crucial for its translocation to the neuronal cytosol, a key ...Botulinum neurotoxin A1 (BoNT/A1) belongs to the most potent toxins and is used as a major therapeutic agent. Neurotoxin conformation is crucial for its translocation to the neuronal cytosol, a key process for intoxication that is only poorly understood. To gain molecular insights into the steps preceding toxin translocation, we determine cryo-EM structures of BoNT/A1 alone and in complex with its receptor synaptic vesicle glycoprotein 2B (SV2B). In solution, BoNT/A1 adopts a unique, semi-closed conformation. The toxin changes its structure into an open state upon receptor binding with the translocation domain (H) and the catalytic domain (LC) remote from the membrane, suggesting translocation incompatibility. Under acidic pH conditions, where translocation is initiated, receptor-bound BoNT/A1 switches back into a semi-closed conformation. This conformation brings the LC and H close to the membrane, suggesting that a translocation-competent state of the toxin is required for successful LC transport into the neuronal cytosol.
History
DepositionApr 23, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50151.png

Downloads & links

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Map

FileDownload / File: emd_50151.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 600 pix.
= 390. Å		0.65 Å/pix.
x 600 pix.
= 390. Å		0.65 Å/pix.
x 600 pix.
= 390. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.5341309 - 0.78166217
Average (Standard dev.)-0.0005038782 (±0.021595338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 390.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50151_msk_1.map
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Additional map: #1

Fileemd_50151_additional_1.map
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Half map: half A

Fileemd_50151_half_map_1.map
Annotationhalf A
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Half map: half B

Fileemd_50151_half_map_2.map
Annotationhalf B
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Sample components

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Entire : Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5

EntireName: Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5
Components
  • Complex: Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5
    • Protein or peptide: Synaptic vesicle glycoprotein 2B
    • Protein or peptide: Botulinum neurotoxin A

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Supramolecule #1: Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5

SupramoleculeName: Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cryo-EM structure of SV2B-BoNT/A1 complex at pH 5.5
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Synaptic vesicle glycoprotein 2B

MacromoleculeName: Synaptic vesicle glycoprotein 2B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDYKYQDNY GGYAPSDGYY RGNESNPEED AQSDVTEGHD EEDEIYEGEY QGIPHPDDVK AKQAKMAPS RMDSLRGQTD LMAERLEDEE QLAHQYETIM DECGHGRFQW ILFFVLGLAL M ADGVEVFV VSFALPSAEK DMCLSSSKKG MLGMIVYLGM MAGAFILGGL ...String:
MDDYKYQDNY GGYAPSDGYY RGNESNPEED AQSDVTEGHD EEDEIYEGEY QGIPHPDDVK AKQAKMAPS RMDSLRGQTD LMAERLEDEE QLAHQYETIM DECGHGRFQW ILFFVLGLAL M ADGVEVFV VSFALPSAEK DMCLSSSKKG MLGMIVYLGM MAGAFILGGL ADKLGRKRVL SM SLAVNAS FASLSSFVQG YGAFLFCRLI SGIGIGGALP IVFAYFSEFL SREKRGEHLS WLG IFWMTG GLYASAMAWS IIPHYGWGFS MGTNYHFHSW RVFVIVCALP CTVSMVALKF MPES PRFLL EMGKHDEAWM ILKQVHDTNM RAKGTPEKVF TVSNIKTPKQ MDEFIEIQSS TGTWY QRWL VRFKTIFKQV WDNALYCVMG PYRMNTLILA VVWFAMAFSY YGLTVWFPDM IRYFQD EEY KSKMKVFFGE HVYGATINFT MENQIHQHGK LVNDKFTRMY FKHVLFEDTF FDECYFE DV TSTDTYFKNC TIESTIFYNT DLYEHKFINC RFINSTFLEQ KEGCHMDLEQ DNDFLIYL V SFLGSLSVLP GNIISALLMD RIGRLKMIGG SMLISAVCCF FLFFGNSESA MIGWQCLFC GTSIAAWNAL DVITVELYPT NQRATAFGIL NGLCKFGAIL GNTIFASFVG ITKVVPILLA AASLVGGGL IALRLPETRE QVLM

UniProtKB: Synaptic vesicle glycoprotein 2B

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Macromolecule #2: Botulinum neurotoxin A

MacromoleculeName: Botulinum neurotoxin A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MRGSHHHHHH GSLVPRGSPF VNKQFNYKDP VNGVDIAYIK IPNAGQMQPV KAFKIHNKIW VIPERDTFTN PEEGDLNPPP EAKQVPVSYY DSTYLSTDNE KDNYLKGVTK LFERIYSTDL GRMLLTSIVR GIPFWGGSTI DTELKVIDTN CINVIQPDGS YRSEELNLVI ...String:
MRGSHHHHHH GSLVPRGSPF VNKQFNYKDP VNGVDIAYIK IPNAGQMQPV KAFKIHNKIW VIPERDTFTN PEEGDLNPPP EAKQVPVSYY DSTYLSTDNE KDNYLKGVTK LFERIYSTDL GRMLLTSIVR GIPFWGGSTI DTELKVIDTN CINVIQPDGS YRSEELNLVI IGPSADIIQF ECKSFGHEVL NLTRNGYGST QYIRFSPDFT FGFEESLEVD TNPLLGAGKF ATDPAVTLAH QLIHAGHRLY GIAINPNRVF KVNTNAYYEM SGLEVSFEEL RTFGGHDAKF IDSLQENEFR LYYYNKFKDI ASTLNKAKSI VGTTASLQYM KNVFKEKYLL SEDTSGKFSV DKLKFDKLYK MLTEIYTEDN FVKFFKVLNA KTFLNFDKAV FKINIVPKVN YTIYDGFNLR NTNLAANFNG QNTEINNMNF TKLKNFTGLF EFYKLLCVRG IITSKTKSLD KGYNKALNDL CIKVNNWDLF FSPSEDNFTN DLNKGEEITS DTNIEAAEEN ISLDLIQQYY LTFNFDNEPE NISIENLSSD IIGQLELMPN IERFPNGKKY ELDKYTMFHY LRAQEFEHGK SRIALTNSVN EALLNPSRVY TFFSSDYVKK VNKATEAAMF LGWVEQLVYD FTDETSEVST TDKIADITII IPYIGPALNI GNMLYKDDFV GALIFSGAVI LLEFIPEIAI PVLGTFALVS YIANKVLTVQ TIDNALSKRN EKWDEVYKYI VTNWLAKVNT QIDLIRKKMK EALENQAEAT KAIINYQYNQ YTEEEKNNIN FNIDDLSSKL NESINKAMIN INKFLNQCSV SYLMNSMIPY GVKRLEDFDA SLKDALLKYI YDNRGTLIGQ VDRLKDKVNN TLSTDIPFQL SKYVDNQRLL STFTEYIKNI INTSILNLRY ESNHLIDLSR YASKINIGSK VNFDPIDKNQ IQLFNLESSK IEVILKNAIV YNSMYENFST SFWIRIPKYF NSISLNNEYT IINCMENNSG WKVSLNYGEI IWTLQDTQEI KQRVVFKYSQ MINISDYINR WIFVTITNNR LNNSKIYING RLIDQKPISN LGNIHASNNI MFKLDGCRDT HRYIWIKYFN LFDKELNEKE IKDLYDNQSN SGILKDFWGD YLQYDKPYYM LNLYDPNKYV DVNNVGIRGY MYLKGPRGSV MTTNIYLNSS LYRGAKFIIK KYASGNKDNI VRNNDRVYIN VVVKNKEYRL ATNASQAGVE KILSALEIPD VGNLSQVVVM KSKNDQGITN KCKMNLQDNN GNDIGFIGFH QFNNIAKLVA SNWYNRQIER SSRTLGCSWE FIPVDDGWGE RPLVPPTPGS AWSHPQFEK

UniProtKB: Botulinum neurotoxin type A

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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: 5.5
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 187001
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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