AF4/FMR2 family member 4 (AFF4) is a 1163-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9UHB7.
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The mean pLDDT of this model is 53.7 (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 | 17% |
| 70 to 90 | Confident: backbone generally right | 7% |
| 50 to 70 | Low: treat with caution | 7% |
| Below 50 | Very low: often disordered regions | 68% |
What pLDDT means and how to read it
Key component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. In the SEC complex, AFF4 acts as a central scaffold that recruits other factors through direct interactions with ELL proteins (ELL, ELL2 or ELL3) and the P-TEFb complex. In case of infection by HIV-1 virus, the SEC complex is recruited by the viral Tat protein to stimulate viral gene expression
Component of the super elongation complex (SEC), at least composed of EAF1, EAF2, CDK9, MLLT3/AF9, AFF (AFF1 or AFF4), the P-TEFb complex and ELL (ELL, ELL2 or ELL3) (PubMed:12065898, PubMed:20159561, PubMed:20471948, PubMed:22195968, PubMed:22483617, PubMed:30134174). Interacts with ELL3; the interaction is direct (By similarity). Interacts with ELL2; the interaction is direct and leads to…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5JW9 | X-ray | 2.0 Å | A=301-351 |
| 6KN5 | X-ray | 2.2 Å | A=899-1163 |
| 6R80 | X-ray | 2.2 Å | A=899-1163 |
| 6K7P | X-ray | 2.4 Å | A=902-1163 |
| 4OR5 | X-ray | 2.9 Å | E/J=32-69 |
| 4IMY | X-ray | 2.94 Å | G/H/I=2-73 |
| 4OGR | X-ray | 3.0 Å | C/G/L=2-73 |
| 6CYT | X-ray | 3.5 Å | C=32-67 |
| 5L1Z | X-ray | 5.9 Å | C=32-67 |
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