Matrix protein VP40 (VP40) is a 326-residue protein from Zaire ebolavirus. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: Q05128.
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The mean pLDDT of this model is 57.7 (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 | 35% |
| 50 to 70 | Low: treat with caution | 33% |
| Below 50 | Very low: often disordered regions | 32% |
What pLDDT means and how to read it
Plays an essential role virus particle assembly and budding (PubMed:16719918, PubMed:33673144). Acts by interacting with viral ribonucleocapsid and host members of the ESCRT (endosomal sorting complex required for transport) system such as host VPS4, PDCD6IP/ALIX, NEDD4 or TGS101 (PubMed:15892969, PubMed:16719918, PubMed:23637409, PubMed:25786915, PubMed:26753796, PubMed:27489272). The interaction with host E3 ubiquitin ligase SMURF2 also facilitates virus budding (PubMed:33673144). May play a role in immune cell dysfunction by being packaged into exosomes that can decrease the viability of recipient cells (via RNAi suppression and exosome-bystander apoptosis) (PubMed:27872619)
Homodimer (PubMed:23953110). Homohexamer (PubMed:11118208, PubMed:23953110). Homooctamer (PubMed:12919741). Exists as a dimer until it reorganizes at the plasma membrane into a hexameric form using phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) (PubMed:23953110, PubMed:25159197, PubMed:26753796, PubMed:29950600). Hexamers are critical for budding (PubMed:23953110). Octamers function in genome…
Host cytoplasm, Host cell membrane, Virion membrane, Host late endosome membrane, Host endomembrane system, Secreted, extracellular exosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7K5L | X-ray | 1.38 Å | A=44-194 |
| 1H2C | X-ray | 1.6 Å | A=55-194 |
| 7K5D | X-ray | 1.78 Å | A=44-194 |
| 4LDM | X-ray | 1.85 Å | A=44-188 |
| 4EJE | X-ray | 2.2 Å | C/D=5-13 |
| 7JZJ | X-ray | 2.46 Å | A/B/C/D=43-326 |
| 1H2D | X-ray | 2.6 Å | A/B=31-212 |
| 4LDB | X-ray | 3.1 Å | A/B/C/D=44-326 |
| 4LDD | X-ray | 3.5 Å | A/B/C=44-326 |
| 7JZT | X-ray | 3.77 Å | A/B/C/D=43-326 |
| 4LDI | X-ray | 4.15 Å | A/B=44-326 |
| 2KQ0 | NMR | B=5-16 |
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