Rabphilin-3A (Rph3a) is a 684-residue protein from Rattus norvegicus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P47709.
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The mean pLDDT of this model is 69.2 (low 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 | 37% |
| 70 to 90 | Confident: backbone generally right | 18% |
| 50 to 70 | Low: treat with caution | 6% |
| Below 50 | Very low: often disordered regions | 39% |
What pLDDT means and how to read it
Plays an essential role in docking and fusion steps of regulated exocytosis (PubMed:16203731, PubMed:8617225). At the presynaptic level, RPH3A is recruited by RAB3A to the synaptic vesicle membrane in a GTP-dependent manner where it modulates synaptic vesicle trafficking and calcium-triggered neurotransmitter release (PubMed:8617225). In the post-synaptic compartment, forms a ternary complex with GRIN2A and DLG4 and regulates NMDA receptor stability (PubMed:26679993). Also plays a role in the exocytosis of arginine vasopressin hormone (PubMed:29367474)
Interacts with RAB3B, RAB3C, RAB3D, RAB8A, RAB27A and RAB27B (By similarity). Interacts with RAB3A; this interaction recruits RPH3A to synaptic vesicules (PubMed:10025402, PubMed:8617225). Interacts (via C2B domain) with SNAP25 (PubMed:16203731, PubMed:28634303). Interacts with deubiquitinating enzyme CAND1; this interaction results in the deubiquitination of RPH3A (PubMed:29367474). Interacts…
Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane, Cell projection, dendritic spine, Postsynaptic cell membrane, Membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2CM5 | X-ray | 1.28 Å | A=519-684 |
| 4NS0 | X-ray | 1.8 Å | A=378-510 |
| 2CM6 | X-ray | 1.85 Å | A/B=519-684 |
| 2CHD | X-ray | 1.92 Å | A=371-510 |
| 4NP9 | X-ray | 1.92 Å | A=378-510 |
| 4LT7 | X-ray | 2.5 Å | A=378-510 |
| 5LO8 | X-ray | 2.5 Å | A/B=536-680 |
| 1ZBD | X-ray | 2.6 Å | B=38-170 |
| 5LOW | X-ray | 2.8 Å | A/B/C/H/I/J=536-680 |
| 5LOB | X-ray | 3.3 Å | A/B/C=536-680 |
| 3RPB | NMR | A=541-680 |
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