Table 1.
FARFAR2-SARS-CoV-2 models
| System | Length | Models generated | Model convergence (Å)a | Predicted minimum RMSD (Å)b | Percent of clusters with < 8.0 REU E-gap to lowest energy modelc | Percent of clusters showing multiple occupancyd |
|---|---|---|---|---|---|---|
| 5′ UTR constructs | ||||||
| 5′ UTR (1–480) | 480 | 66011 | 50.9 | 44.92 ± 6.13 | 20% | 0% |
| 5′ UTR stem–loop 1 (7–33) | 27 | 200000 | 1.83 | 5.17 ± 0.52 | 100% | 100% |
| 5′ UTR stem–loop 2 (45–59) | 15 | 200000 | 2.39 | 5.63 ± 0.74 | 100% | 100% |
| 5′ UTR stem–loop 3 (61–75) | 15 | 200000 | 2.58 | 5.78 ± 0.70 | 100% | 100% |
| 5′ UTR stem–loop 4 (84–127) | 44 | 2018457 | 1.82 | 5.16 ± 0.49 | 100% | 80% |
| 5′ UTR stem–loop 5 (148–295) | 148 | 2392320 | 18.99 | 19.07 ± 6.15 | 100% | 10% |
| 5′ UTR stem–loop 5/6 (148–343) | 196 | 2020963 | 25.91 | 24.68 ± 6.27 | 50% | 10% |
| 5′ UTR stem–loop 6 (302–343) | 42 | 200000 | 8.92 | 10.92 ± 2.21 | 100% | 100% |
| 5′ UTR stem–loop 7 (349–394) | 27 | 200000 | 7.39 | 9.67 ± 1.90 | 20% | 100% |
| 5′ UTR stem–loop 8 (407–478) | 72 | 4055322 | 6.86 | 9.24 ± 1.47 | 70% | 100% |
| 5′ UTR reverse complement | ||||||
| 5′ UTR reverse complement stem–loops 1–4 (149–1) | 149 | 2031710 | 19.61 | 19.57 ± 4.37 | 90% | 0% |
| Frameshift stimulating element constructs | ||||||
| Frameshift stimulating element (13459–13546) | 88 | 390722 | 14.45 | 15.39 ± 3.09 | 80% | 80% |
| Suspected frameshift stimulating element dimer (13459–13546) | 176 | 23066 | 21.99 | 21.50 ± 4.08 | 30% | 0% |
| 3′ UTR constructs | ||||||
| 3′ UTR beginning with bulged hairpin (29511–29871) | 361 | 11430 | 39.71 | 35.85 ± 5.51 | 20% | 0% |
| 3′ UTR hypervariable region (29659–29852) | 194 | 28029 | 25.38 | 24.25 ± 4.18 | 80% | 0% |
| 3′ UTR pseudoknot (29543–29665; 29846–29876) | 158 | 1017205 | 21.93 | 21.45 ± 5.52 | 100% | 0% |
| 3′ UTR pseudoknot fragment consisting of the pseudoknot (PK), P2, and P6 (29606–29665; 29846–29876) | 95 | 1017205 | 10.24 | 11.99 ± 2.05 | 100% | 50% |
| 3′ UTR BSL extended structure (29543–29665; 29846–29876) | 158 | 1012716 | 24.04 | 23.16 ± 4.29 | 100% | 0% |
| 3′ UTR stem–loop II-like motif, homology modeled from PDB ID: 1XJR (12) (29724–29773) | 50 | 200000 | 6.95 | 9.32 ± 0.09 | 50% | 100% |
| 3′ UTR stem–loop II-like motif, secondary structure based on NMR data from Wacker et al. (38) (29724–29773) | 50 | 500000 | 2.97 | 6.10 ± 0.75 | 100% | 10% |
aMean pairwise all-heavy-atom RMSD between 10 lowest energy cluster centers discovered.
bPredicted RMSD to true structure.
cRosetta all-atom free energy gap of cluster's lowest energy model compared to lowest energy model discovered in run. REU = Rosetta energy units, calibrated so that 1.0 corresponds approximately to 1 kBT.
dPercent of clusters with more than one cluster member. Clustering was carried out on top 400 models ranked by Rosetta all-atom free energy, based on 5.0 Å threshold, except for small RNAs (SL1–4, SL6–7, s2m), where 2.0 Å threshold was applied.