Histone H4 (HHF1) is a 103-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P02309.
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The mean pLDDT of this model is 88.1 (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 | 73% |
| 70 to 90 | Confident: backbone generally right | 7% |
| 50 to 70 | Low: treat with caution | 18% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. Together with SPT15/TBP UAF seems to stimulate basal transcription to a fully…
The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Histone H4 is a component of the UAF (upstream activation factor) complex which consists of UAF30, RRN5, RRN9, RRN10, and histones H3 and H4
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6RXK | X-ray | 1.35 Å | B=13-23 |
| 1Q1A | X-ray | 1.5 Å | B=13-22 |
| 1SZD | X-ray | 1.5 Å | B=13-22 |
| 6RXJ | X-ray | 1.6 Å | C/D=13-22 |
| 4TWJ | X-ray | 1.65 Å | B=9-21 |
| 6RXQ | X-ray | 1.7 Å | E/F/G/H=13-23 |
| 6RXR | X-ray | 1.7 Å | E/F/G/H=13-23 |
| 1SZC | X-ray | 1.75 Å | B=13-22 |
| 4TWI | X-ray | 1.79 Å | B=9-21 |
| 6RXP | X-ray | 1.8 Å | C/D=13-23 |
| 1E6I | X-ray | 1.87 Å | P=16-30 |
| 6RXM | X-ray | 1.92 Å | G/H/I/J/K/L=13-23 |
| 6RXO | X-ray | 1.95 Å | C/D=13-23 |
| 2QQF | X-ray | 2.0 Å | B=13-23 |
| 2DVQ | X-ray | 2.04 Å | P/Q=2-16 |
| 2QQG | X-ray | 2.05 Å | B=13-23 |
| 3TO6 | X-ray | 2.1 Å | B=12-23 |
| 2H2H | X-ray | 2.2 Å | B=76-86 |
| 2DVR | X-ray | 2.3 Å | P/Q=2-16 |
| 2E3K | X-ray | 2.3 Å | Q/R=2-16 |
Showing 20 of 55 experimental structures (best resolution first).
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