Histone H4 (LOC121398084) is a 116-residue protein from Xenopus laevis. This is its AlphaFold structure prediction, created 31 Mar 2025. UniProt accession: A0A8J1LTD2.
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The mean pLDDT of this model is 82.8 (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 | 65% |
| 70 to 90 | Confident: backbone generally right | 7% |
| 50 to 70 | Low: treat with caution | 17% |
| Below 50 | Very low: often disordered regions | 11% |
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
Chromosome, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9JNP | EM | 2.3 Å | B/F=15-116 |
| 9JNU | EM | 2.5 Å | B/F=15-116 |
| 9JNT | EM | 2.7 Å | B/F=15-116 |
| 9LIU | EM | 2.7 Å | B/F=15-116 |
| 9JO5 | EM | 2.8 Å | B/F=15-116 |
| 8UW1 | EM | 2.88 Å | B/F=14-116 |
| 9JNW | EM | 2.9 Å | B/F=15-116 |
| 9JNV | EM | 3.0 Å | B/F=15-116 |
| 9JNX | EM | 3.0 Å | B/F=15-116 |
| 9JNZ | EM | 3.0 Å | B/F=15-116 |
| 9JO2 | EM | 3.0 Å | B/F=15-116 |
| 9QIK | EM | 3.03 Å | G/H=14-116 |
| 9CAN | EM | 3.3 Å | B/F=14-116 |
| 8SKZ | EM | 3.5 Å | F/I=14-116 |
| 9KQ2 | EM | 3.9 Å | B/F=15-116 |
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