Botulinum neurotoxin type A (botA) is a 1296-residue protein from Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0DPI1.
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The mean pLDDT of this model is 92.1 (very high overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 79% |
| 70 to 90 | Confident: backbone generally right | 17% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Botulinum toxin causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of the eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure (PubMed:8103915). Precursor of botulinum neurotoxin A which has 2 coreceptors; complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins of synaptic vesicles (By similarity). Receptor proteins are exposed on host presynaptic cell membrane during neurotransmitter release, when the toxin heavy chain (HC) binds to them (PubMed:19476346). Upon synaptic vesicle recycling the toxin is taken up via the…
Heterodimer; disulfide-linked heterodimer of a light chain (LC) and a heavy chain (HC) (PubMed:17173035, PubMed:9783750). Interacts with host synaptic vesicle glycoproteins SV2A, SV2B and SV2C which serve as coreceptors (By similarity). Glycosylation of 'Asn-559' in SV2C probably contributes a 12-fold increase in affinity to this interaction (By similarity). Depolarization of target tissue with…
Secreted, Host cytoplasm, host cytosol, Host synapse, host presynaptic cell membrane, Host cytoplasmic vesicle, host secretory vesicle, host synaptic vesicle membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4EL4 | X-ray | 1.2 Å | A=1-425 |
| 3C8B | X-ray | 1.47 Å | A=1-424 |
| 3DDA | X-ray | 1.5 Å | A=1-424 |
| 3QW7 | X-ray | 1.5 Å | A=1-424 |
| 3C8A | X-ray | 1.52 Å | A=1-424 |
| 3C89 | X-ray | 1.58 Å | A=1-424 |
| 3C88 | X-ray | 1.6 Å | A=1-424 |
| 3DDB | X-ray | 1.6 Å | A=1-424 |
| 3QW5 | X-ray | 1.6 Å | A=1-424 |
| 3QW6 | X-ray | 1.6 Å | A=1-424 |
| 3QW8 | X-ray | 1.6 Å | A=1-424 |
| 5L21 | X-ray | 1.68 Å | A=872-1296 |
| 3BWI | X-ray | 1.7 Å | A=1-424 |
| 4KUF | X-ray | 1.7 Å | A=1-425 |
| 3DS9 | X-ray | 1.76 Å | A=1-417 |
| 3FUO | X-ray | 1.8 Å | A=871-1296 |
| 4ELC | X-ray | 1.8 Å | A=1-425 |
| 4EJ5 | X-ray | 1.87 Å | A=1-425 |
| 3DSE | X-ray | 1.9 Å | A=1-417 |
| 4KS6 | X-ray | 1.93 Å | A=1-425 |
Showing 20 of 38 experimental structures (best resolution first).
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