Histone H3-like centromeric protein A (CENPA) is a 140-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P49450.
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The mean pLDDT of this model is 81.5 (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 | 60% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 30% |
| Below 50 | Very low: often disordered regions | 4% |
What pLDDT means and how to read it
Histone H3-like nucleosomal protein that is specifically found in centromeric nucleosomes (PubMed:11756469, PubMed:14667408, PubMed:15282608, PubMed:15475964, PubMed:15702419, PubMed:17651496, PubMed:19114591, PubMed:20739937, PubMed:27499292, PubMed:7962047, PubMed:9024683). Replaces conventional H3 in the nucleosome core of centromeric chromatin that serves as an assembly site for the inner kinetochore (PubMed:18072184). The presence of CENPA subtly modifies the nucleosome structure and the way DNA is wrapped around the nucleosome and gives rise to protruding DNA ends that are less well-ordered and rigid compared to nucleosomes containing histone H3 (PubMed:26878239, PubMed:27499292).…
Component of centromeric nucleosomes, where DNA is wrapped around a histone octamer core (PubMed:20739937, PubMed:21743476, PubMed:23818633, PubMed:26878239). The octamer contains two molecules each of H2A, H2B, CENPA and H4 assembled in one CENPA-H4 heterotetramer and two H2A-H2B heterodimers (PubMed:20739937, PubMed:21743476, PubMed:23818633, PubMed:26878239). CENPA modulates the DNA-binding…
Nucleus, Chromosome, centromere
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5CVD | X-ray | 1.3 Å | D/E=3-10 |
| 6KDQ | X-ray | 1.5 Å | E/F=2-8 |
| 6KDS | X-ray | 1.84 Å | E=2-7 |
| 3NQJ | X-ray | 2.1 Å | A=60-140 |
| 7R5R | EM | 2.44 Å | A/E=1-140 |
| 3NQU | X-ray | 2.5 Å | A=1-140 |
| 5ZBX | X-ray | 2.58 Å | A/E=79-116 |
| 3R45 | X-ray | 2.6 Å | A=1-140 |
| 6E0P | EM | 2.6 Å | A/E=1-140 |
| 6E0C | EM | 2.63 Å | A/E=1-140 |
| 3WTP | X-ray | 2.67 Å | A=1-140 |
| 7PII | EM | 2.68 Å | A/E=1-140 |
| 7U46 | EM | 2.68 Å | A/E=1-140 |
| 5Z23 | X-ray | 2.73 Å | A/E=75-116 |
| 7D20 | EM | 3.0 Å | A/E=1-140 |
| 6SEG | EM | 3.1 Å | A/E=1-140 |
| 6O1D | EM | 3.4 Å | A/E=1-140 |
| 6MUP | EM | 3.5 Å | A/E=38-139 |
| 6SE6 | EM | 3.5 Å | A/E=1-140 |
| 3AN2 | X-ray | 3.6 Å | A/E=1-140 |
Showing 20 of 34 experimental structures (best resolution first).
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