Histone H3.3 (HTR4) is a 136-residue protein from Arabidopsis thaliana. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P59169.
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The mean pLDDT of this model is 86.0 (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 | 68% |
| 70 to 90 | Confident: backbone generally right | 5% |
| 50 to 70 | Low: treat with caution | 25% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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…
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. The H3K9meK27me dimethylated N-terminal tail of histone H3 can directly interact with the chromodomains of CMT3 and/or LHP1. Interacts with AHL27. Binds to HIRA (PubMed:25086063)
Nucleus, Chromosome, Nucleus, nucleolus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4PLI | X-ray | 1.65 Å | C/D=32-42 |
| 4PL6 | X-ray | 1.68 Å | C/D=2-12 |
| 8XAG | X-ray | 1.75 Å | C/D=26-33 |
| 4PLL | X-ray | 2.6 Å | C/D=32-42 |
| 9K45 | EM | 2.71 Å | A/E=1-136 |
| 9K46 | EM | 2.85 Å | A/E=1-136 |
| 7UX9 | EM | 3.2 Å | E/F=1-136 |
| 9K44 | EM | 3.22 Å | A/E=1-136 |
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