Histone H2A.Z (H2AZ1) is a 128-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0C0S5.
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The mean pLDDT of this model is 90.4 (very high 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 | 81% |
| 70 to 90 | Confident: backbone generally right | 5% |
| 50 to 70 | Low: treat with caution | 10% |
| Below 50 | Very low: often disordered regions | 5% |
What pLDDT means and how to read it
Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. 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. May be involved in the formation of constitutive heterochromatin. May be required for chromosome segregation during cell division
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. H2A or its variant H2AZ1 forms a heterodimer with H2B. H2AZ1 interacts with INCENP (By similarity). Interacts (via M6 cassette) with ANP32E; leading to removal of H2A.Z/H2AZ1 from the…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4CAY | X-ray | 1.48 Å | A=19-128 |
| 6KO2 | X-ray | 1.5 Å | B=4-10 |
| 5CHL | X-ray | 1.89 Å | B=22-113 |
| 9INC | X-ray | 2.01 Å | A/D=17-114 |
| 6JOU | X-ray | 2.17 Å | C/G=1-128 |
| 5B31 | X-ray | 2.2 Å | G=1-128 |
| 5B32 | X-ray | 2.35 Å | G=1-128 |
| 5Z30 | X-ray | 2.45 Å | C/G=1-128 |
| 9UBD | X-ray | 2.53 Å | A/D=17-114 |
| 1F66 | X-ray | 2.6 Å | C/G=1-128 |
| 8T9F | EM | 2.6 Å | C/G=1-128 |
| 4NFT | X-ray | 2.61 Å | A/B/C/D=16-114 |
| 5FUG | X-ray | 2.7 Å | A/D/G/J=19-128 |
| 9OGR | EM | 2.78 Å | C/G=2-128 |
| 9OH0 | EM | 2.78 Å | C/G=2-128 |
| 5B33 | X-ray | 2.92 Å | C/G=1-128 |
| 9OGS | EM | 3.05 Å | C/G=2-128 |
| 9OGZ | EM | 3.05 Å | C/G=2-128 |
| 3WA9 | X-ray | 3.07 Å | C/G=1-128 |
| 9OH1 | EM | 3.09 Å | C/G=2-128 |
Showing 20 of 28 experimental structures (best resolution first).
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