Histone H3.1 (H3C1) is a 136-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P68431.
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The mean pLDDT of this model is 86.1 (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 | 68% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 27% |
| Below 50 | Very low: often disordered regions | 1% |
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 (PubMed:36435862). The octamer wraps approximately 147 bp of DNA. Interacts with TONSL; CHAF1A; CHAF1B; MCM2 and DNAJC9 (PubMed:33857403). Interacts with NASP; NASP is a histone chaperone that stabilizes and maintains a soluble pool of…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5SVY | X-ray | 1.05 Å | B=2-12 |
| 2V89 | X-ray | 1.1 Å | D/E=2-11 |
| 5SZC | X-ray | 1.19 Å | H=2-19 |
| 5SZB | X-ray | 1.2 Å | H=2-19 |
| 6BHD | X-ray | 1.25 Å | B=4-20 |
| 4UP0 | X-ray | 1.28 Å | F=2-16 |
| 5FFV | X-ray | 1.3 Å | C/D=10-20 |
| 5WXH | X-ray | 1.3 Å | D/P=2-8 |
| 4L7X | X-ray | 1.35 Å | U=2-13 |
| 6BHE | X-ray | 1.35 Å | B=4-20 |
| 6BHI | X-ray | 1.4 Å | B=5-20 |
| 5TDR | X-ray | 1.42 Å | B=2-12 |
| 2RI7 | X-ray | 1.45 Å | P=2-10 |
| 4X3K | X-ray | 1.45 Å | C/D=24-30 |
| 5GH9 | X-ray | 1.45 Å | B=45-58 |
| 6BHG | X-ray | 1.45 Å | B=4-20 |
| 3V43 | X-ray | 1.47 Å | Q=2-19 |
| 5JIY | X-ray | 1.48 Å | F/G=4-14 |
| 8IJ0 | X-ray | 1.52 Å | C/D=2-12 |
| 3RIY | X-ray | 1.55 Å | C/D=5-16 |
Showing 20 of 532 experimental structures (best resolution first).
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