E3 ubiquitin-protein ligase RNF4 (Rnf4) is a 194-residue protein from Rattus norvegicus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O88846.
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The mean pLDDT of this model is 72.3 (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 | 30% |
| 70 to 90 | Confident: backbone generally right | 12% |
| 50 to 70 | Low: treat with caution | 52% |
| Below 50 | Very low: often disordered regions | 7% |
What pLDDT means and how to read it
E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates 'Lys-6'-, 'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation (PubMed:14987998, PubMed:15707587, PubMed:18408734). Regulates the degradation of several proteins including PML and the transcriptional activator PEA3 (PubMed:15707587, PubMed:20943951). Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation (By similarity). Regulates the cellular responses to hypoxia and heat shock…
Homodimer (via RING-type zinc finger domain) (PubMed:20681948). Interacts with GSC2 (By similarity). Interacts with AR/the androgen receptor and TBP (PubMed:9710597). Interacts with TCF20 (By similarity). Interacts with PATZ1. Interacts with TRPS1; negatively regulates TRPS1 transcriptional repressor activity. Interacts with PML (isoform PML-1, isoform PML-2, isoform PML-3, isoform PML-4,…
Cytoplasm, Nucleus, Nucleus, nucleoplasm, Nucleus, PML body
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3NG2 | X-ray | 1.8 Å | A/B=124-194 |
| 4AP4 | X-ray | 2.21 Å | A=131-194 |
| 5AIU | X-ray | 2.21 Å | A=131-194 |
| 5AIT | X-ray | 3.4 Å | A=131-194 |
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