Nucleoplasmin is a 200-residue protein from Xenopus laevis. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P05221.
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The mean pLDDT of this model is 74.3 (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 | 45% |
| 70 to 90 | Confident: backbone generally right | 8% |
| 50 to 70 | Low: treat with caution | 26% |
| Below 50 | Very low: often disordered regions | 21% |
What pLDDT means and how to read it
Acts as a chaperone for histones, such as histone H2A-H2B, and thus regulates the assembly of nucleosome cores (PubMed:11684019, PubMed:19055325). Involved in chromatin remodeling, especially during fertilization and early embryonic development (By similarity). May be involved in sperm chromatin decondensation during fertilization (PubMed:17510054)
Homopentamer, when bound to H2A-H2B dimers only. Homodecamer of two stacked pentamers, when bound to H2A-H2B dimers and H3-H4 tetramers simultaneously. Interacts with the heterotetramer formed by wdr77 and prmt5
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3UL1 | X-ray | 1.9 Å | A=153-172 |
| 1K5J | X-ray | 2.3 Å | A/B/C/D/E=1-124 |
| 4BPL | X-ray | 2.3 Å | B=152-172 |
| 1EE5 | X-ray | 2.4 Å | B=153-171 |
| 2VTX | X-ray | 2.5 Å | A/B/C/D/E/G/H/I/J/K=1-120 |
| 1EJY | X-ray | 2.9 Å | N=155-170 |
| 8VHI | EM | 5.0 Å | A/B/C/D/E=1-200 |
| 8VHK | EM | 5.16 Å | A/B/C/D/E=1-200 |
| 8VHJ | EM | 5.9 Å | A/B/C/D/E=1-200 |
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