Presenilin-1 (PSEN1) is a 467-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P49768.
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The mean pLDDT of this model is 72.1 (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 | 36% |
| 70 to 90 | Confident: backbone generally right | 25% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 27% |
What pLDDT means and how to read it
Catalytic subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors and APP (amyloid-beta precursor protein) (PubMed:10206644, PubMed:10545183, PubMed:10593990, PubMed:10811883, PubMed:10899933, PubMed:12679784, PubMed:12740439, PubMed:15274632, PubMed:20460383, PubMed:25043039, PubMed:26280335, PubMed:28269784, PubMed:30598546, PubMed:30630874). Requires the presence of the other members of the gamma-secretase complex for protease activity (PubMed:15274632, PubMed:25043039, PubMed:26280335, PubMed:30598546, PubMed:30630874). Plays a role in Notch and Wnt signaling cascades and regulation…
Homodimer. The functional gamma-secretase complex is composed of at least four polypeptides: a presenilin homodimer (PSEN1 or PSEN2), nicastrin (NCSTN), APH1 (APH1A/APH1B) and PEN2 (PubMed:12679784, PubMed:12740439, PubMed:15274632, PubMed:25043039, PubMed:25394380, PubMed:26280335, PubMed:30598546, PubMed:30630874). Such minimal complex is sufficient for secretase activity (PubMed:12679784,…
Endoplasmic reticulum, Endoplasmic reticulum membrane, Golgi apparatus membrane, Cytoplasmic granule, Cell membrane, Cell projection, growth cone, Early endosome, Early endosome membrane, Cell projection, neuron projection, Cell projection, axon, Synapse
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8KCS | EM | 2.4 Å | B=1-467 |
| 6IYC | EM | 2.6 Å | B=1-467 |
| 7D8X | EM | 2.6 Å | B=1-467 |
| 8K8E | EM | 2.6 Å | B=1-467 |
| 8KCT | EM | 2.6 Å | B=1-467 |
| 6IDF | EM | 2.7 Å | B=1-467 |
| 8KCU | EM | 2.7 Å | B=1-467 |
| 8KCO | EM | 2.8 Å | B=1-467 |
| 7Y5T | EM | 2.9 Å | B=1-467 |
| 8X52 | EM | 2.9 Å | B=1-467 |
| 8X54 | EM | 2.9 Å | B=1-467 |
| 9K95 | EM | 2.9 Å | B=1-467 |
| 6LR4 | EM | 3.0 Å | B=1-467 |
| 8KCP | EM | 3.0 Å | B=1-467 |
| 8X53 | EM | 3.0 Å | B=1-467 |
| 6LQG | EM | 3.1 Å | B=1-467 |
| 7C9I | EM | 3.1 Å | B=1-467 |
| 8OQY | EM | 3.3 Å | B=1-467 |
| 5A63 | EM | 3.4 Å | B=1-467 |
| 8IM7 | EM | 3.4 Å | B=1-467 |
Showing 20 of 27 experimental structures (best resolution first).
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