Epstein-Barr nuclear antigen 2 (EBNA2) is a 487-residue protein from Epstein-Barr virus. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P12978.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 45.4 (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 | 3% |
| 70 to 90 | Confident: backbone generally right | 9% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 75% |
What pLDDT means and how to read it
Plays a key role in the activation of the host resting B-cell and stimulation of B-cell proliferation. Acts by up-regulating the expression of viral EBNA1-6, LMP1, LMP2A and LMP2B genes, as well as several host genes including CD21, CD23 and MYC. Activates transcription by acting as an adapter molecule that binds to cellular sequence-specific DNA-binding proteins such as host CBF1, SMARCB1 and SPI1. Once EBNA2 is near promoter sites, its acidic activating domain recruits basal and activation-associated transcription factors TFIIB, TAF40, TFIIH components ERCC2 and ERCC3, and CBP in order to promote transcription. Alternatively, EBNA2 can affect activities of cell cycle regulators and…
Interacts with human SMARCB1/INI1, presumably generating an open chromatin conformation at the EBNA2-responsive target genes (PubMed:8709224). Interacts with human WAPL (PubMed:15383329). Interacts with host CBF1; this interaction allows transcriptional activation by EBNA2 (PubMed:8016657). Interacts with host general transcription factors GTF2B, ERCC2 and ERCC3 (PubMed:7724549, PubMed:7983760).…
Host nucleus matrix
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5HDA | X-ray | 2.39 Å | B/D=381-389 |
| 9D96 | X-ray | 2.4 Å | C=14-23 |
| 9D95 | X-ray | 2.8 Å | C/H/M/R=14-23 |
| 2MKR | NMR | B=453-465 | |
| 2N2J | NMR | A/B=1-58 |
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.