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- EMDB-50166: Focused refinement of SV2B-LD-BoNT/A1 at pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-50166
TitleFocused refinement of SV2B-LD-BoNT/A1 at pH 5.5
Map data
Sample
  • Complex: SV2B-BoNT/A1 complex at pH 5.5
    • Protein or peptide: Synaptic vesicle glycoprotein 2B
    • Protein or peptide: Botulinum neurotoxin type A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordstransporter / botulinum neurotoxin / synaptic vesicle glycoprotein / Membrane protein / TOXIN
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 speciesHomo sapiens (human) / Clostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.39 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 24, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50166.png

Downloads & links

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Map

FileDownload / File: emd_50166.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.5027899 - 2.8045115
Average (Standard dev.)-0.0005354905 (±0.02302048)
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_50166_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_50166_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_50166_half_map_2.map
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Sample components

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Entire : SV2B-BoNT/A1 complex at pH 5.5

EntireName: SV2B-BoNT/A1 complex at pH 5.5
Components
  • Complex: SV2B-BoNT/A1 complex at pH 5.5
    • Protein or peptide: Synaptic vesicle glycoprotein 2B
    • Protein or peptide: Botulinum neurotoxin type A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SV2B-BoNT/A1 complex at pH 5.5

SupramoleculeName: SV2B-BoNT/A1 complex at pH 5.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: SV2B-BoNT/A1 complex at pH 5.5
Source (natural)Organism: Homo sapiens (human)
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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.515016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDYKYQDNY GGYAPSDGYY RGNESNPEED AQSDVTEGHD EEDEIYEGEY QGIPHPDDVK AKQAKMAPSR MDSLRGQTDL MAERLEDEE QLAHQYETIM DECGHGRFQW ILFFVLGLAL MADGVEVFVV SFALPSAEKD MCLSSSKKGM LGMIVYLGMM A GAFILGGL ...String:
MDDYKYQDNY GGYAPSDGYY RGNESNPEED AQSDVTEGHD EEDEIYEGEY QGIPHPDDVK AKQAKMAPSR MDSLRGQTDL MAERLEDEE QLAHQYETIM DECGHGRFQW ILFFVLGLAL MADGVEVFVV SFALPSAEKD MCLSSSKKGM LGMIVYLGMM A GAFILGGL ADKLGRKRVL SMSLAVNASF ASLSSFVQGY GAFLFCRLIS GIGIGGALPI VFAYFSEFLS REKRGEHLSW LG IFWMTGG LYASAMAWSI IPHYGWGFSM GTNYHFHSWR VFVIVCALPC TVSMVALKFM PESPRFLLEM GKHDEAWMIL KQV HDTNMR AKGTPEKVFT VSNIKTPKQM DEFIEIQSST GTWYQRWLVR FKTIFKQVWD NALYCVMGPY RMNTLILAVV WFAM AFSYY GLTVWFPDMI RYFQDEEYKS KMKVFFGEHV YGATINFTME NQIHQHGKLV NDKFTRMYFK HVLFEDTFFD ECYFE DVTS TDTYFKNCTI ESTIFYNTDL YEHKFINCRF INSTFLEQKE GCHMDLEQDN DFLIYLVSFL GSLSVLPGNI ISALLM DRI GRLKMIGGSM LISAVCCFFL FFGNSESAMI GWQCLFCGTS IAAWNALDVI TVELYPTNQR ATAFGILNGL CKFGAIL GN TIFASFVGIT KVVPILLAAA SLVGGGLIAL RLPETREQVL M

UniProtKB: Synaptic vesicle glycoprotein 2B

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Macromolecule #2: Botulinum neurotoxin type A

MacromoleculeName: Botulinum neurotoxin type A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 153.083734 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MRGSHHHHHH GSLVPRGSPF VNKQFNYKDP VNGVDIAYIK IPNAGQMQPV KAFKIHNKIW VIPERDTFTN PEEGDLNPPP EAKQVPVSY YDSTYLSTDN EKDNYLKGVT KLFERIYSTD LGRMLLTSIV RGIPFWGGST IDTELKVIDT NCINVIQPDG S YRSEELNL ...String:
MRGSHHHHHH GSLVPRGSPF VNKQFNYKDP VNGVDIAYIK IPNAGQMQPV KAFKIHNKIW VIPERDTFTN PEEGDLNPPP EAKQVPVSY YDSTYLSTDN EKDNYLKGVT KLFERIYSTD LGRMLLTSIV RGIPFWGGST IDTELKVIDT NCINVIQPDG S YRSEELNL VIIGPSADII QFECKSFGHE VLNLTRNGYG STQYIRFSPD FTFGFEESLE VDTNPLLGAG KFATDPAVTL AH QLIHAGH RLYGIAINPN RVFKVNTNAY YEMSGLEVSF EELRTFGGHD AKFIDSLQEN EFRLYYYNKF KDIASTLNKA KSI VGTTAS LQYMKNVFKE KYLLSEDTSG KFSVDKLKFD KLYKMLTEIY TEDNFVKFFK VLNAKTFLNF DKAVFKINIV PKVN YTIYD GFNLRNTNLA ANFNGQNTEI NNMNFTKLKN FTGLFEFYKL LCVRGIITSK TKSLDKGYNK ALNDLCIKVN NWDLF FSPS EDNFTNDLNK GEEITSDTNI EAAEENISLD LIQQYYLTFN FDNEPENISI ENLSSDIIGQ LELMPNIERF PNGKKY ELD KYTMFHYLRA QEFEHGKSRI ALTNSVNEAL LNPSRVYTFF SSDYVKKVNK ATEAAMFLGW VEQLVYDFTD ETSEVST TD KIADITIIIP YIGPALNIGN MLYKDDFVGA LIFSGAVILL EFIPEIAIPV LGTFALVSYI ANKVLTVQTI DNALSKRN E KWDEVYKYIV TNWLAKVNTQ IDLIRKKMKE ALENQAEATK AIINYQYNQY TEEEKNNINF NIDDLSSKLN ESINKAMIN INKFLNQCSV SYLMNSMIPY GVKRLEDFDA SLKDALLKYI YDNRGTLIGQ VDRLKDKVNN TLSTDIPFQL SKYVDNQRLL STFTEYIKN IINTSILNLR YESNHLIDLS RYASKINIGS KVNFDPIDKN QIQLFNLESS KIEVILKNAI VYNSMYENFS T SFWIRIPK YFNSISLNNE YTIINCMENN SGWKVSLNYG EIIWTLQDTQ EIKQRVVFKY SQMINISDYI NRWIFVTITN NR LNNSKIY INGRLIDQKP ISNLGNIHAS NNIMFKLDGC RDTHRYIWIK YFNLFDKELN EKEIKDLYDN QSNSGILKDF WGD YLQYDK PYYMLNLYDP NKYVDVNNVG IRGYMYLKGP RGSVMTTNIY LNSSLYRGAK FIIKKYASGN KDNIVRNNDR VYIN VVVKN KEYRLATNAS QAGVEKILSA LEIPDVGNLS QVVVMKSKND QGITNKCKMN LQDNNGNDIG FIGFHQFNNI AKLVA SNWY NRQIERSSRT LGCSWEFIPV DDGWGERPLV PPTPGSAWSH PQFEK

UniProtKB: Botulinum neurotoxin type A

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AB-intiao reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187001
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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