General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 (RAD3) is a 778-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P06839.
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The mean pLDDT of this model is 85.8 (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 | 45% |
| 70 to 90 | Confident: backbone generally right | 48% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
ATP-dependent 5'-3' DNA helicase (PubMed:25775526, PubMed:2827162). Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to TFIIK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. The ATP-dependent helicase activity of XPD/RAD3 is required for DNA opening. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH…
Component of the 7-subunit TFIIH core complex composed of XPB/SSL2, XPD/RAD3, SSL1, TFB1, TFB2, TFB4 and TFB5, which is active in NER. The core complex associates with the 3-subunit CTD-kinase module TFIIK composed of CCL1, KIN28 and TFB3 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription (PubMed:7961739, PubMed:7813015, PubMed:14500720). An additional subunit, TFB6, plays a…
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7O4J | EM | 2.9 Å | 0=1-778 |
| 7ML0 | EM | 3.0 Å | 0=1-778 |
| 8CEN | EM | 3.0 Å | 0=1-778 |
| 7ML4 | EM | 3.1 Å | 0=1-778 |
| 7ZS9 | EM | 3.1 Å | 0=1-778 |
| 7O4I | EM | 3.2 Å | 0=1-778 |
| 7O75 | EM | 3.2 Å | 0=1-778 |
| 7ML2 | EM | 3.4 Å | 0=1-778 |
| 7O4L | EM | 3.4 Å | 0=1-778 |
| 7O72 | EM | 3.4 Å | 0=1-778 |
| 7O73 | EM | 3.4 Å | 0=1-778 |
| 7O4K | EM | 3.6 Å | 0=1-778 |
| 8CEO | EM | 3.6 Å | 0=1-778 |
| 8UMI | EM | 3.7 Å | 0=1-778 |
| 8UOT | EM | 3.7 Å | 0=1-778 |
| 8UOQ | EM | 3.8 Å | 0=1-778 |
| 7K01 | EM | 3.9 Å | 0=1-778 |
| 7ML1 | EM | 4.0 Å | 0=1-778 |
| 7ZSA | EM | 4.0 Å | 0=1-778 |
| 8UMH | EM | 4.1 Å | 0=1-778 |
Showing 20 of 29 experimental structures (best resolution first).
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