Nuclear protein localization protein 4 (NPL4) is a 580-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P33755.
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The mean pLDDT of this model is 91.6 (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 | 80% |
| 70 to 90 | Confident: backbone generally right | 15% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 4% |
What pLDDT means and how to read it
Substrate-recruiting cofactor of the CDC48-NPL4-UFD1 segregase (PubMed:31249135). Assists CDC48 in the dislocation of misfolded, polyubiquitinated ERAD substrates that are subsequently delivered to the proteasome for degradation (PubMed:11739805, PubMed:11740563, PubMed:11847109). Involved in the import of nuclear-targeted proteins into the nucleus and the export of poly(A) RNA out of the nucleus (PubMed:11733065, PubMed:8930904). Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1 (PubMed:11733065). Regulates ubiquitin-mediated mitochondria protein degradation (PubMed:31249135). Involved in…
Component of the heterotrimeric CDC48-NPL4-UFD1 ATPase complex (PubMed:16873066). The CDC48-NPL4-UFD1 ATPase complex interacts with the HRD1 ubiquitin ligase complex composed of the E3 ligase HRD1, its cofactors HRD3, USA1 and DER1, substrate recruiting factor YOS9 and CDC48-binding protein UBX2 (PubMed:16873066). Interaction between the complexes is mediated by interaction between…
Cytoplasm, perinuclear region, Endoplasmic reticulum membrane, Nucleus membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6JWJ | X-ray | 1.58 Å | A=113-580 |
| 6JWH | X-ray | 1.72 Å | A=113-580 |
| 6JWI | X-ray | 2.55 Å | A/E=113-580 |
| 8DAR | EM | 3.0 Å | G=1-580 |
| 9OFV | EM | 3.16 Å | G=1-580 |
| 8DAS | EM | 3.5 Å | G=1-580 |
| 8DAV | EM | 3.5 Å | G=1-580 |
| 8DAW | EM | 3.6 Å | G=1-580 |
| 8DAU | EM | 3.7 Å | G=1-580 |
| 8DAT | EM | 3.8 Å | G=1-580 |
| 6OA9 | EM | 3.9 Å | G=1-580 |
| 6OAA | EM | 4.1 Å | G=1-580 |
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