Gamma-secretase subunit APH-1A (APH1A) is a 265-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q96BI3.
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The mean pLDDT of this model is 91.8 (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 | 77% |
| 70 to 90 | Confident: backbone generally right | 15% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Non-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:12297508, PubMed:12522139, PubMed:12679784, PubMed:12763021, PubMed:25043039, PubMed:26280335, PubMed:30598546, PubMed:30630874). Required for normal gamma-secretase assembly (PubMed:12471034, PubMed:12522139, PubMed:12763021, PubMed:19369254). The gamma-secretase complex plays a role in Notch and Wnt signaling cascades and regulation of downstream processes via its role in processing key regulatory proteins, and by regulating cytosolic CTNNB1 levels (Probable)
The functional gamma-secretase complex is composed of at least four polypeptides: a presenilin homodimer (PSEN1 or PSEN2), nicastrin (NCSTN), APH1 (APH1A or APH1B) and PSENEN/PEN2 (PubMed:12297508, PubMed:12740439, PubMed:19369254, PubMed:25043039, PubMed:26280335, PubMed:26623517, PubMed:30598546, PubMed:30630874)
Endoplasmic reticulum membrane, Golgi apparatus, Golgi stack membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8KCS | EM | 2.4 Å | C=1-265 |
| 6IYC | EM | 2.6 Å | C=1-265 |
| 7D8X | EM | 2.6 Å | C=1-265 |
| 8K8E | EM | 2.6 Å | C=1-265 |
| 8KCT | EM | 2.6 Å | C=1-265 |
| 6IDF | EM | 2.7 Å | C=1-265 |
| 8KCU | EM | 2.7 Å | C=1-265 |
| 8KCO | EM | 2.8 Å | C=1-265 |
| 7Y5T | EM | 2.9 Å | C=1-265 |
| 8X52 | EM | 2.9 Å | C=1-265 |
| 8X54 | EM | 2.9 Å | C=1-265 |
| 9K95 | EM | 2.9 Å | C=1-265 |
| 6LR4 | EM | 3.0 Å | C=1-265 |
| 7Y5X | EM | 3.0 Å | C=1-265 |
| 8KCP | EM | 3.0 Å | C=1-265 |
| 8X53 | EM | 3.0 Å | C=1-265 |
| 6LQG | EM | 3.1 Å | C=1-265 |
| 7C9I | EM | 3.1 Å | C=1-265 |
| 5A63 | EM | 3.4 Å | C=1-265 |
| 7Y5Z | EM | 3.4 Å | C=1-265 |
Showing 20 of 25 experimental structures (best resolution first).
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