Major capsid protein L1 (L1) is a 505-residue protein from Human papillomavirus type 16. This is its AlphaFold structure prediction, created 3 Sept 2026. UniProt accession: P03101.
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The mean pLDDT of this model is 83.9 (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 | 55% |
| 70 to 90 | Confident: backbone generally right | 29% |
| 50 to 70 | Low: treat with caution | 10% |
| Below 50 | Very low: often disordered regions | 7% |
What pLDDT means and how to read it
Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2
Self-assembles into homopentamers. The capsid has an icosahedral symmetry and consists of 72 capsomers, with each capsomer being a pentamer of L1. Interacts with the minor capsid protein L2; this interaction is necessary for viral genome encapsidation. Interacts with protein E2; this interaction enhances E2-dependent replication and transcription activation (PubMed:25911730). Interacts with host…
Virion, Host nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8XES | X-ray | 1.78 Å | C=386-394 |
| 9NZU | EM | 1.9 Å | A/B/C/D/E/F=1-485 |
| 8XFZ | X-ray | 2.32 Å | C=27-35 |
| 7KZF | EM | 3.1 Å | A/B/C/D/E/F=1-503 |
| 7CN2 | EM | 3.43 Å | A/B/C/D/E/F=1-505 |
| 1DZL | X-ray | 3.5 Å | A=1-505 |
| 5KEP | EM | 4.3 Å | A/B/C/D/E/F=3-485 |
| 5KEQ | EM | 4.3 Å | A/B/C/D/E/F=3-485 |
| 6BSP | EM | 4.7 Å | C/D/E/F/G/H=12-480 |
| 6BT3 | EM | 4.7 Å | I/J/K/L/M/N=1-503 |
| 3J6R | EM | 9.1 Å | A/B/C/D/E/F=9-486 |
| 3JBA | EM | 12.0 Å | A/B/C/D/E/F=9-486 |
| 3J8W | EM | 13.0 Å | A/B/C/D/E=21-474 |
| 3J7G | EM | 13.6 Å | A/B/C/D/E=21-474 |
| 3J8V | EM | 13.9 Å | A/B/C/D/E=21-474 |
| 3J8Z | EM | 14.0 Å | A/B/C/D/E=21-474 |
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