Table 1.
Key Protein Data Bank (PDB) entries used in generating structural models representing different viral RNA-dependent RNA polymerase nucleotide addition cycle (RdRP NAC) states and a list of related PDB entries.
| NAC State | PDB(s) for Model Construction | Reference PDB(s) | Active Site Conformation |
|---|---|---|---|
| 1 | 5F8G (EV71) | 3OL6, 4K4S, 4K4T, 4K4U, 4K4V, 4K4W, 4K4X, 4K4Z, 4K50, 5F8G, 5F8L [12,14,15] | Open |
| 2 | 5F8H (EV71), 3OLB (PV) a | 3OLA (chains I/M), 3OLB, 4K4Y, 5F8H [12,15] | Open |
| 2/3 | 5F8I (EV71) | 5F8I [15] | Partially closed |
| 3 | 5F8J (EV71), 3BSO (NV) b | 3BSO [16] | Closed |
| 4 | 5F8M (EV71) | 3OL7, 3OL8, 5F8J, 5F8M [12,15] | Closed |
| 5 | 5F8G (EV71), 3OL9 (PV) c | 3OL9, 3OLA (chains A/E) [12] | Open |
| 6 | 5F8N (EV71) | 5F8N [15] | Open |
a The model was generated using the polymerase and RNA chains from entry 5F8H and a CTP molecule modeled based on the ddCTP molecule from entry 3OLB; b The model was generated using the polymerase and RNA chains from entry 5F8J with the +1 nucleotide removed and the CTP molecule and the catalytic manganese ions from entry 3BSO; c The model was generated using the polymerase and RNA chains from entry 5F8G with the last two nucleotides at the 3′-end of the product strand modeled based on entry 3OL9. PV: poliovirus; NV: norovirus.