Minor capsid protein L2 (L2) is a 473-residue protein from Human papillomavirus type 16. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P03107.
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The mean pLDDT of this model is 60.1 (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 | 14% |
| 70 to 90 | Confident: backbone generally right | 18% |
| 50 to 70 | Low: treat with caution | 22% |
| Below 50 | Very low: often disordered regions | 46% |
What pLDDT means and how to read it
Minor protein of the capsid that localizes along the inner surface of the virion, within the central cavities beneath the L1 pentamers. Plays a role in capsid stabilization through interaction with the major capsid protein L1. Once the virion enters the host cell, L2 escorts the genomic DNA into the nucleus by promoting escape from the endosomal compartments and traffic through the host Golgi network. Mechanistically, the C-terminus of L2 possesses a cell-penetrating peptide that protudes from the host endosome, interacts with host cytoplasmic retromer cargo and thereby mediates the capsid delivery to the host trans-Golgi network. Plays a role through its interaction with host dynein in…
Interacts with major capsid protein L1. Interacts with E2; this interaction inhibits E2 transcriptional activity but not the DNA replication function E2. Interacts with host GADD45GIP1. Interacts with host HSPA8; this interaction is required for L2 nuclear translocation. Interacts with host importins KPNB2 and KPNB3. Forms a complex with importin alpha2-beta1 heterodimers via interaction with…
Virion, Host nucleus, Host early endosome, Host Golgi apparatus
UniProt lists no experimental PDB structure for this protein, so the AlphaFold prediction is the main 3D model available.
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