Regulator of nonsense transcripts 1 (UPF1) is a 1129-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q92900.
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The mean pLDDT of this model is 72.8 (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 | 41% |
| 70 to 90 | Confident: backbone generally right | 25% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 29% |
What pLDDT means and how to read it
RNA-dependent helicase required for nonsense-mediated decay (NMD) of aberrant mRNAs containing premature stop codons and which modulates the expression level of normal mRNAs (PubMed:11163187, PubMed:16086026, PubMed:18172165, PubMed:21145460, PubMed:21419344, PubMed:24726324). ATP-dependent 5'-3' helicase active on RNA:DNA substrates with a 5'-RNA extension (PubMed:18066079, PubMed:21419344, PubMed:23275559, PubMed:26138914). ATP-dependent 5'-3' helicase active on RNA:RNA substrates with a 5'-RNA extension (PubMed:26138914). ATP-dependent 5'-3' helicase active on DNA:DNA substrates with a 5'-DNA extension (PubMed:10999600, PubMed:26138914, PubMed:30218034). Is recruited to mRNAs upon…
Monomeric in solution (PubMed:10999600, PubMed:26138914). Forms a trimeric UPF complex where UPF2 bridges UPF1 and UPF3B; UPF2 contacts the N-terminal CH-rich domain of UPF1 and the N-terminus of UPF3B (PubMed:18066079). The trimeric UPF complex interacts with the EJC core complex (PubMed:18066079). Found in a post-splicing messenger ribonucleoprotein (mRNP) complex (PubMed:21419344). Associates…
Cytoplasm, Cytoplasm, P-body, Nucleus, Cytoplasm, perinuclear region
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2GK6 | X-ray | 2.4 Å | A/B=295-925 |
| 2XZO | X-ray | 2.4 Å | A=295-925 |
| 2WJY | X-ray | 2.5 Å | A=115-925 |
| 2GJK | X-ray | 2.6 Å | A=295-925 |
| 8RXB | X-ray | 2.6 Å | A/D/E/I/L/P=115-287 |
| 2XZP | X-ray | 2.72 Å | A=295-925 |
| 2GK7 | X-ray | 2.8 Å | A=295-925 |
| 2WJV | X-ray | 2.85 Å | A/B=115-925 |
| 2IYK | X-ray | 2.95 Å | A/B=115-272 |
| 6Z3R | EM | 2.97 Å | E=1085-1095 |
| 6EJ5 | X-ray | 3.34 Å | A=295-925 |
| 9QWN | EM | 3.6 Å | A=115-925 |
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