Histone H3.1 (HTR2) is a 136-residue protein from Arabidopsis thaliana. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P59226.
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The mean pLDDT of this model is 86.4 (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 | 6% |
| 50 to 70 | Low: treat with caution | 24% |
| 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
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 (PubMed:11898023, PubMed:15457214). Interacts with ORTH2…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6LQF | X-ray | 1.5 Å | P=2-16 |
| 5YVX | X-ray | 1.59 Å | C=2-10 |
| 9M4S | X-ray | 1.6 Å | P=2-11 |
| 9M4R | X-ray | 1.7 Å | P=2-11 |
| 7DE9 | X-ray | 1.71 Å | P=2-16 |
| 5HH7 | X-ray | 1.9 Å | P=2-16 |
| 5ZWX | X-ray | 1.9 Å | P/Q=2-16 |
| 6LQE | X-ray | 1.9 Å | P=2-16 |
| 5Z8L | X-ray | 2.0 Å | P=21-36 |
| 5VBC | X-ray | 2.1 Å | C/D=24-37 |
| 8JG4 | X-ray | 2.3 Å | C/D=25-32 |
| 7YTA | X-ray | 2.31 Å | P/Q/R=2-16 |
| 5VAH | X-ray | 2.4 Å | C/D=22-36 |
| 7CCE | X-ray | 2.4 Å | P=21-38 |
| 4IUR | X-ray | 2.5 Å | C=2-16 |
| 5YC3 | X-ray | 2.6 Å | P=2-10 |
| 6IP4 | X-ray | 2.6 Å | B=25-36 |
| 4FT4 | X-ray | 2.7 Å | P/Q=2-33 |
| 4IUT | X-ray | 2.7 Å | C=2-16 |
| 4IUU | X-ray | 2.7 Å | C=2-16 |
Showing 20 of 43 experimental structures (best resolution first).
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