Epstein-Barr nuclear antigen 1 (EBNA1) is a 641-residue protein from Epstein-Barr virus. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P03211.
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The mean pLDDT of this model is 41.4 (very low 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 | 0% |
| 70 to 90 | Confident: backbone generally right | 14% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 82% |
What pLDDT means and how to read it
Responsible for the origin of replication (oriP) dependent replication and maintenance of viral episomes during latent infection (PubMed:15479791, PubMed:2996781). EBNA1 dimer interacts with the DS (dyad symmetry) element within the origin of replication oriP and with a host mitotic chromosome to initiate viral DNA replication during latency (PubMed:24067969, PubMed:2996781, PubMed:31142669, PubMed:8551585). EBNA1 binding to DS recruits the host origin recognition complex (ORC) (PubMed:12953058). Governs the faithful mitotic segregation of the viral episomes by binding both the FR (family of repeats) element within oriP and the host mitotic chromosomes (PubMed:11172042, PubMed:15479791,…
Homodimer (PubMed:19521517, PubMed:9878348). Dimers can assemble into higher-order oligomers like a homohexamer (PubMed:28701406). Binding to the DS element involves 2 dimers of EBNA1 (PubMed:14506283, PubMed:15808506, PubMed:18833293, PubMed:31142669). Interacts with human USP7; this interaction is independent and simultaneous to EBNA1 interaction with CSNK2B as well as necessary for PML…
Host nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6VH6 | X-ray | 1.3 Å | A/B=470-607 |
| 6NPP | X-ray | 1.35 Å | A=471-607 |
| 2FYY | X-ray | 1.5 Å | C=407-417 |
| 6NPI | X-ray | 1.5 Å | A/B=471-607 |
| 6NPM | X-ray | 1.6 Å | A/B=471-607 |
| 4PRE | X-ray | 1.65 Å | C=407-417 |
| 1YY6 | X-ray | 1.7 Å | B=441-450 |
| 4PRA | X-ray | 1.85 Å | C=407-417 |
| 2FZ3 | X-ray | 1.9 Å | C=407-417 |
| 5WMF | X-ray | 1.9 Å | A/B/C/D/E/F=470-619 |
| 3MV7 | X-ray | 2.0 Å | C=407-417 |
| 5WUM | X-ray | 2.0 Å | B/C=378-386 |
| 3MV8 | X-ray | 2.1 Å | C=407-417 |
| 1B3T | X-ray | 2.2 Å | A/B=461-607 |
| 5WUN | X-ray | 2.2 Å | B/C=378-386 |
| 7KE3 | X-ray | 2.2 Å | A/B/C/D/E/F/G/H/I/J/K/L=407-417 |
| 5T7X | X-ray | 2.35 Å | A/B=459-607 |
| 4PRI | X-ray | 2.4 Å | C=407-417 |
| 1VHI | X-ray | 2.5 Å | A/B=466-607 |
| 4PRP | X-ray | 2.5 Å | C=407-417 |
Showing 20 of 26 experimental structures (best resolution first).
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