Histone H2A.6 (RAT5) is a 130-residue protein from Arabidopsis thaliana. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9LD28.
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The mean pLDDT of this model is 89.9 (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 | 79% |
| 70 to 90 | Confident: backbone generally right | 5% |
| 50 to 70 | Low: treat with caution | 14% |
| 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. Required for the T-DNA integration step of plant transformation by Agrobacterium. May play an important role in illegitimate recombination
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. Interacts with VIP1
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7BP2 | X-ray | 1.58 Å | A/C=14-106 |
| 7BP6 | X-ray | 1.58 Å | C=14-106 |
| 7BP5 | X-ray | 1.9 Å | A=14-106 |
| 7BP4 | X-ray | 2.1 Å | A/G=14-106 |
| 7C7X | X-ray | 3.0 Å | A/C=14-106 |
| 9K42 | EM | 3.14 Å | C/G=1-130 |
| 9K40 | EM | 3.15 Å | C/G=1-130 |
| 8KCB | EM | 3.17 Å | A/B=1-130 |
| 8WHB | EM | 3.17 Å | C/G=1-130 |
| 9K44 | EM | 3.22 Å | C/G=1-130 |
| 8WH9 | EM | 3.31 Å | C/G=1-130 |
| 8WH5 | EM | 3.58 Å | C/G=1-130 |
| 8WH8 | EM | 3.6 Å | C/G=1-130 |
| 8WHA | EM | 4.05 Å | C/G=1-130 |
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