Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (PDE6A) is a 859-residue protein from Bos taurus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P11541.
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The mean pLDDT of this model is 90.0 (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 | 75% |
| 70 to 90 | Confident: backbone generally right | 20% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Catalytic alpha subunit of the rod-specific cGMP phosphodiesterase (PDE6) complex, which hydrolyzes 3',5'-cyclic GMP in the phototransduction cascade. The PDE6 holoenzyme consists of two catalytic subunits (PDE6A and PDE6B) and two inhibitory gamma subunits (PDE6G) (PubMed:33007200, PubMed:38159849). Light-activated GNAT1 relieves gamma subunit-mediated inhibition, enabling the catalytic subunits to hydrolyze cGMP and thereby mediate visual signal transduction and amplification (PubMed:33007200, PubMed:38159849). Decreased cytosolic cGMP levels result in closure of cGMP-gated cation channels at the plasma membrane, leading to rod photoreceptor hyperpolarization (Probable)
Tetramer composed of two catalytic chains (alpha and beta) and two inhibitory chains (gamma) (PubMed:38159849). Interacts with GNAT1; two GNAT1-GTP molecules bind both the catalytic core (PDE6A and PDE6B) and the inhibitory PDE6G subunits, inducing conformational rearrangements that relieve inhibition and activate catalysis (PubMed:33007200, PubMed:38159849)
Photoreceptor outer segment membrane, Cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8UGB | EM | 3.0 Å | A=1-859 |
| 8UFI | EM | 3.1 Å | A=1-859 |
| 7JSN | EM | 3.2 Å | A=1-859 |
| 8UGS | EM | 3.2 Å | A=1-859 |
| 8ULG | EM | 3.2 Å | A=1-859 |
| 6MZB | EM | 3.4 Å | A=1-859 |
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