Runt-related transcription factor 3 (RUNX3) is a 415-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q13761.
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The mean pLDDT of this model is 60.6 (low 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 | 28% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 56% |
What pLDDT means and how to read it
Forms the heterodimeric complex core-binding factor (CBF) with CBFB. RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'-TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX. The heterodimers bind to the core site of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL3 and GM-CSF promoters (By similarity). May be involved in the control of cellular proliferation and/or…
Heterodimer with CBFB. RUNX3 binds DNA as a monomer and through the Runt domain. DNA-binding is increased by heterodimerization (By similarity). Interacts with TLE1 and SUV39H1 (PubMed:16652147, PubMed:9751710). The tyrosine phosphorylated form (via runt domain) interacts with SRC (via protein kinase domain) (PubMed:20100835). Interacts with FYN and LCK (PubMed:20100835). Interacts with FOXP3…
Nucleus, Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5W69 | X-ray | 2.8 Å | I/J/K/L=133-141 |
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