TABLE 1.
Results obtained by fitting the crystallographic structure components into the cryoEM map
| Protein | Modela | Sumf (%) | Clash (%) | Density (%) | Avg distance (Å) | Orientation
|
Center
|
||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| θ1 | θ2 | θ3 | x | y | z | ||||||
| E1 | SFV E1 (Cα) | 43.4 | 0.7 | 0.1 | 17.2 | 189.8 | 85.5 | 171.0 | 28.4 | 77.3 | 283.5 |
| SINV E1 (Cα) | 41.6 | 1.2 | 1.0 | 16.2 | 189.0 | 85.8 | 170.8 | 27.9 | 77.3 | 283.5 | |
| TBEV E (Cα) | 29.3 | 0.0 | 14.1 | 18.7 | 153.5 | 89.2 | 49.5 | 27.4 | 69.8 | 283.5 | |
| SINV E1 (all) | 37.4 | 0.5 | 4.4 | 14.5 | 187.0 | 85.2 | 170.8 | 28.4 | 78.8 | 283.5 | |
| E2 | SFV E1 (Cα) | 30.3 | 1.4 | 8.1 | 21.3 | 22.5 | 55.5 | 46.1 | 12.0 | 92.8 | 289.8 |
| TM | GCN4 (Cα, trunc) | 31.9 | 0.0 | 1.8 | 16.3 | 132.2 | 78.0 | 106.2 | 4.5 | 48.8 | 238.0 |
| GCN4 (Cα, ext) | 26.1 | 0.0 | 13.6 | — | 132.2 | 78.0 | 106.2 | 3.0 | 54.3 | 253.2 | |
| CP | CP (Cα) | 45.1 | 1.2 | 0.3 | — | 99.0 | 106.5 | 140.5 | 8.7 | 44.0 | 192.0 |
| CP + pep (Cα) | 45.0 | 0.6 | 0.3 | 9.5 | 99.5 | 107.2 | 140.0 | 8.7 | 44.0 | 192.5 | |
| CP (all) | 40.1 | 0.1 | 3.6 | — | 97.5 | 108.0 | 139.5 | 8.7 | 44.5 | 191.5 | |
| CP + pep (all) | 40.2 | 0.1 | 3.6 | 9.9 | 98.5 | 108.0 | 138.5 | 8.2 | 44.0 | 192.0 | |
| CP (old fit, all) | 35.1 | 5.8 | 8.0 | — | — | 8.2 | 41.5 | 192.0 | |||
Cα indicates that only Cα atoms were used; all indicates that main chain and side chain atoms were used; trunc indicates that only residues 250 to 277 were used for fitting; ext indicates that the entire GCN4 structure was used; + pep shows that a peptide (residues 108 to 110) was added to the capsid protein (CP) structure in the binding pocket. The previously determined orientation from Ross River virus (8) was used without change for the CP (old fit, all). However, the positions were refined to account for a slightly different estimated pixel size. SFV, Semliki Forest virus; SINV, Sindbis virus; TBEV, tick-borne encephalitis virus. Results were obtained by using the EMfit program (45).