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- PDB-9f3c: Low-resolution (5.4 angstrom) cryo-EM structure of SV2B-BoNT/A1 a... -

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Basic information

Entry
Database: PDB / ID: 9f3c
TitleLow-resolution (5.4 angstrom) cryo-EM structure of SV2B-BoNT/A1 at pH 5.5
Components
  • Botulinum neurotoxin type A
  • Synaptic vesicle glycoprotein 2B
KeywordsMEMBRANE PROTEIN / transporter / botulinum neurotoxin / synaptic vesicle glycoprotein
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.41 Å
AuthorsKhanppnavar, B. / Leka, O. / Korkhov, V. / Kammerer, R.
Funding support Switzerland, 2items
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 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptic vesicle glycoprotein 2B
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,6285
Polymers230,5992
Non-polymers1,0293
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Synaptic vesicle glycoprotein 2B


Mass: 77515.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SV2B, KIAA0735 / Production host: Homo sapiens (human) / References: UniProt: Q7L1I2
#2: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX / Botulinum neurotoxin type A1


Mass: 153083.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bonT
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DPI0
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1SV2B-BoNT/A1 complex at pH 5.5COMPLEXSV2B-BoNT/A1 complex at pH 5.5#1-#20MULTIPLE SOURCES
2Synaptic vesicle glycoprotein 2BCOMPLEX#11RECOMBINANT
3Botulinum neurotoxin type ACOMPLEX#21RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Clostridium botulinum (bacteria)1491
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187001 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Details: The SV2B transmembrane domain from PDB ID: 951R and SV2B-LD-BoNT/A1 complex from PDB: 9F2Y were docked and refined on low resolution map
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
19F1R

9f1r

19F1R1PDBexperimental model
29F2Y

9f2y

19F2Y2PDBexperimental model

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