Structural polyprotein is a 1253-residue protein from Semliki forest virus. This is its AlphaFold structure prediction, created 3 Jul 2025. UniProt accession: P03315.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 75.7 (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 | 24% |
| 70 to 90 | Confident: backbone generally right | 50% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 14% |
What pLDDT means and how to read it
Forms an icosahedral capsid with a T=4 symmetry composed of 240 copies of the capsid protein surrounded by a lipid membrane through which penetrate 80 spikes composed of trimers of E1-E2 heterodimers (PubMed:16407067). The capsid protein binds to the viral RNA genome at a site adjacent to a ribosome binding site for viral genome translation following genome release (By similarity). Possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein (PubMed:3553612, PubMed:9642067). Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles…
Homodimer (By similarity). Homomultimer (By similarity). Interacts with host karyopherin KPNA4; this interaction allows the nuclear import of the viral capsid protein (By similarity). Interacts with spike glycoprotein E2 (By similarity). Interacts with host IRAK1; the interaction leads to inhibition of IRAK1-dependent signaling (By similarity)
Virion, Host cytoplasm, Host cell membrane, Host nucleus, Virion membrane, Host Golgi apparatus, Host Golgi apparatus, host trans-Golgi network, Host endoplasmic reticulum
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2V33 | X-ray | 1.55 Å | A/B=1107-1197 |
| 1I9W | X-ray | 3.0 Å | A=816-1205 |
| 1VCP | X-ray | 3.0 Å | A/B/C=119-267 |
| 2ALA | X-ray | 3.0 Å | A=816-1206 |
| 8IHP | EM | 3.0 Å | A/D/G/J=334-755, B/E/H/K=816-1253, C/F/I/L=106-267 |
| 8YVY | EM | 3.02 Å | A/F/G/H=816-1253, B/I/J/K=338-755, C/L/M/N=275-326, D/O/P/Q=107-267 |
| 1VCQ | X-ray | 3.1 Å | A/B=119-267 |
| 1RER | X-ray | 3.2 Å | A/B/C=816-1206 |
| 8D87 | EM | 3.2 Å | A/B/C=816-1206 |
| 8YW1 | EM | 3.44 Å | A/E/F/G/H/U/V/W=816-1253, B/I/J/K/R/X/Y/Z=338-755, D/O/P/Q/T/d/e/f=107-267, L/M/N/S/a/b/c/g=275-326 |
| 8YVZ | EM | 3.45 Å | A/F/G/H=816-1253, B/I/J/K=338-755, C/L/M/N=275-326, D/O/P/Q=107-267 |
| 8X0K | EM | 3.5 Å | A/E/I/M=106-267, B/F/J/N=334-751, C/G/K/O=816-1253 |
| 8X0L | EM | 3.5 Å | A/E/I=106-267, B/F/J=334-751, C/G/K=816-1253 |
| 8X0M | EM | 3.5 Å | A/E/I=106-267, B/F/J=334-751, C/G/K=816-1253 |
| 8YW0 | EM | 3.55 Å | A/F/G/H=816-1253, B/I/J/K=338-755, C/L/M/N=275-326, D/O/P/Q=107-267 |
| 8UA8 | EM | 3.7 Å | A/E/I/M=816-1253, B/F/J/N=339-755, C/G/K=275-325, D/H/L/P=116-267, O=273-325 |
| 8YW2 | EM | 3.7 Å | 0/2/AA/AB/L/M/N/S/a/b/c/g/l/u/v/w=275-326, 1/3/AC/AD/AE/D/O/P/Q/T/d/e/f/n/x/y=107-267, 4/5/6/E/F/G/H/U/V/W/h/i/m/o/p/q=816-1253, 7/8/9/B/I/J/K/R/X/Y/Z/j/r/s/t/z=338-755 |
| 9KQR | EM | 3.73 Å | a/d/g/j=816-1253 |
| 1DYL | EM | 9.0 Å | A/B/C/D=119-267 |
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