Synaptotagmin-1 (Syt1) is a 421-residue protein from Rattus norvegicus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P21707.
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The mean pLDDT of this model is 81.8 (confident 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 | 55% |
| 70 to 90 | Confident: backbone generally right | 22% |
| 50 to 70 | Low: treat with caution | 7% |
| Below 50 | Very low: often disordered regions | 15% |
What pLDDT means and how to read it
Calcium sensor that participates in triggering neurotransmitter release at the synapse (PubMed:2333096, PubMed:30107533). May have a regulatory role in the membrane interactions during trafficking of synaptic vesicles at the active zone of the synapse. It binds acidic phospholipids with a specificity that requires the presence of both an acidic head group and a diacyl backbone. A Ca(2+)-dependent interaction between synaptotagmin and putative receptors for activated protein kinase C has also been reported. It can bind to at least three additional proteins in a Ca(2+)-independent manner; these are neurexins, syntaxin and AP2. Plays a role in dendrite formation by melanocytes
Homotetramer (Probable). Heterodimer; heterodimerizes with SYT2 in presence of calcium (PubMed:9867811). Interacts with SCAMP5 (By similarity). Interacts with STON2 (By similarity). Forms a complex with SV2B, syntaxin 1 and SNAP25 (By similarity). Interacts with SV2A, SV2B and SV2C (PubMed:15866046, PubMed:8910372). Interacts with RIMS1 (PubMed:11438518). Interacts with PRRT2 (By similarity).…
Cytoplasmic vesicle, secretory vesicle membrane, Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane, Cytoplasmic vesicle, secretory vesicle, chromaffin granule membrane, Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4WEE | X-ray | 0.89 Å | A=140-266 |
| 1TJX | X-ray | 1.04 Å | A=271-421 |
| 1UOW | X-ray | 1.04 Å | A=271-421 |
| 1TJM | X-ray | 1.18 Å | A=271-421 |
| 2YOA | X-ray | 1.5 Å | A/B=271-421 |
| 1UOV | X-ray | 1.65 Å | A=271-421 |
| 5CCJ | X-ray | 1.65 Å | A/B/C/D=271-421 |
| 8C5H | X-ray | 1.68 Å | S=142-265 |
| 6CXW | X-ray | 1.83 Å | A=140-182, A=201-265 |
| 5W5C | X-ray | 1.85 Å | F=140-421 |
| 1RSY | X-ray | 1.9 Å | A=127-266 |
| 5W5D | X-ray | 2.5 Å | F=270-421 |
| 5CCG | X-ray | 3.5 Å | E/F/K=141-421 |
| 5KJ7 | X-ray | 3.5 Å | E/F/K=141-419 |
| 5CCH | X-ray | 3.6 Å | E/F=141-421 |
| 5CCI | X-ray | 4.1 Å | E/F=141-421 |
| 5KJ8 | X-ray | 4.1 Å | E/F/K=141-419 |
| 6MTI | EM | 10.4 Å | 1/6=141-267, 2/3/4/5=141-421 |
| 1BYN | NMR | A=140-267 | |
| 1K5W | NMR | A=270-421 |
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