ORF3a protein (3a) is a 275-residue protein from Severe acute respiratory syndrome coronavirus 2. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P0DTC3.
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The mean pLDDT of this model is 55.5 (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 | 0% |
| 70 to 90 | Confident: backbone generally right | 28% |
| 50 to 70 | Low: treat with caution | 30% |
| Below 50 | Very low: often disordered regions | 42% |
What pLDDT means and how to read it
Plays a role in viral egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion channels (viroporins) localized at endosomes and lysosomes, that may induce deacidification of lysosomes, allowing safe egress of virions via lysosomal trafficking (PubMed:33157038, PubMed:33422265, PubMed:34158638). Also blocks autolysosome formation by binding and sequestering the host component VPS39 for homotypic fusion and protein sorting (HOPS) on late endosomes (PubMed:33422265). This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress (PubMed:33422265). Induces host RETREG1/FAM134B-dependent reticulophagy by interacting…
Homodimer (PubMed:34158638), a subset forms homotetramer of two homodimers linked non covalently (PubMed:34158638). Interacts with M, S and E proteins. Also interacts with the accessory protein 7a (By similarity). Interacts with host VPS39, sequestering it on late endosomes (PubMed:33422265). Interacts with host HMGB1; the interaction enhances the association between HMGB1 and host BECN1,…
Virion, Host cell membrane, Host endoplasmic reticulum membrane, Secreted, Host cytoplasm, Host endosome, Host lysosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8T5Q | X-ray | 1.9 Å | G/H/I=36-40 |
| 7KJR | EM | 2.08 Å | A/B=1-275 |
| 8T5P | X-ray | 2.5 Å | G/H/I=36-40 |
| 8EQU | EM | 2.8 Å | A/B=1-275 |
| 6XDC | EM | 2.9 Å | A/B=1-275 |
| 8EQJ | EM | 3.0 Å | A/B=1-275 |
| 9RU5 | EM | 3.26 Å | P=207-215 |
| 8EQT | EM | 3.4 Å | A/B=1-275 |
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