General negative regulator of transcription subunit 1 (CDC39) is a 2108-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P25655.
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The mean pLDDT of this model is 78.0 (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 | 21% |
| 70 to 90 | Confident: backbone generally right | 60% |
| 50 to 70 | Low: treat with caution | 9% |
| Below 50 | Very low: often disordered regions | 10% |
What pLDDT means and how to read it
Acts as a component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover. The NOT protein subcomplex negatively regulates the basal and activated transcription of many genes. Preferentially affects TC-type TATA element-dependent transcription. Could directly or indirectly inhibit component(s) of the general transcription machinery
Forms a NOT protein complex that comprises NOT1, NOT2, NOT3, NOT4 and NOT5. Subunit of the 1.0 MDa CCR4-NOT core complex that contains CCR4, CAF1, NOT1, NOT2, NOT3, NOT4, NOT5, CAF40 and CAF130. In the complex interacts with CCR4, POP2, NOT2, NOT4 and NOT5. The core complex probably is part of a less characterized 1.9 MDa CCR4-NOT complex
Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4B89 | X-ray | 1.5 Å | A=755-1000 |
| 4B8A | X-ray | 2.4 Å | A=755-1000 |
| 4B8B | X-ray | 2.8 Å | A/B=151-753 |
| 4BY6 | X-ray | 2.8 Å | A/D=1541-2093 |
| 4B8C | X-ray | 3.41 Å | B/G/H/I=755-1000 |
| 5AJD | X-ray | 3.62 Å | A/C/E/G/I/K=1541-2093 |
| 4CV5 | X-ray | 3.81 Å | A/C=1071-1282 |
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