Table A1.
List of PDB identifiers associated with ssRNA phages’ structures. This list excludes PDB related to replicase structures.
| Phages | PDB# | Method | Brief Description |
|---|---|---|---|
| Culturable ssRNA phages | |||
| MS2 | 2MS2 | X-ray | T = 3 VLP |
| 1BMS | X-ray | T = 3 VLP (P78N) | |
| 1MST | X-ray | T = 3 VLP (E76D) | |
| 1ZDI | X-ray | CP/RNA complex, WT RNA | |
| 1ZDH | X-ray | CP/RNA complex, C-5 variant RNA (U→C mutant) | |
| 1AQ3 | X-ray | CP(T59S)/RNA complex | |
| 1AQ4 | X-ray | CP(T45A)/RNA complex | |
| 1MVA | X-ray | T = 3 VLP, CP(T45A) | |
| 1MVB | X-ray | T = 3 VLP, CP(T59S) | |
| 1ZDJ | X-ray | CP/RNA complex, loop RNA (5′-GGAUCACC-3′), shorter RNA operator derived from WT RNA operator | |
| 1ZDK | X-ray | CP/RNA complex, clamp RNA, elongated stem of C-5 variant RNA operator | |
| 6MSF | X-ray | CP/RNA complex, F6 RNA, derived from WT and C-5 version | |
| 5MSF | X-ray | CP/RNA complex, F5 RNA, derived from WT and C-5 version | |
| 7MSF | X-ray | CP/RNA complex, F7 RNA, derived from WT and C-5 version | |
| 1U1Y | X-ray | CP/RNA complex, F5 RNA with 2-aminopurine at -10 position | |
| 2BU1 | X-ray | CP/RNA complex, RNA operator with 5-bromouracil at -5 position | |
| 2C4Q | X-ray | CP/RNA complex, RNA operator with pyridin-2-one at -5 position | |
| 2C4Y | X-ray | CP/RNA complex, RNA operator with 2-thiouracil at -5 position | |
| 2C4Z | X-ray | CP/RNA complex, RNA operator with 2-thiouracil at -5 and -6 position | |
| 2C50 | X-ray | CP/RNA complex, RNA operator with adenine at -5 position | |
| 2C51 | X-ray | CP/RNA complex, RNA operator with guanine at -5 position | |
| 2BNY | X-ray | CP(N87A)/ MS2 RNA complex | |
| 2BQ5 | X-ray | CP(N87A/E89K)/MS2 RNA complex | |
| 2BS0 | X-ray | CP(N87A/E89K)/variant Qβ RNA complex | |
| 2BS1 | X-ray | CP(N87A/E89K)/Qβ RNA complex | |
| 1ZSE | X-ray | CP(N87S)/Qβ RNA complex | |
| 2B2D | X-ray | CP(N87S/E89K)/Qβ RNA complex | |
| 2B2E | X-ray | CP(N87S/E89K)/MS2 RNA complex | |
| 2B2G | X-ray | CP(N87S)/MS2 RNA complex | |
| 2IZ8 | X-ray | CP/RNA complex, C-5 RNA operator with cytosine at -7 position | |
| 2IZ9 | X-ray | CP/RNA complex, RNA operator with pyridin-4-one at -5 position | |
| 2IZN | X-ray | CP/RNA complex, RNA operator with guanine at -10 position, and GC pairs above and below -10 position changed to CG | |
| 2IZM | X-ray | CP/RNA complex, C-5 RNA operator with cytosine at -10 position | |
| 2VTU | X-ray | Octahedral VLP (artifact) from covalent CP dimer fusion | |
| 4ZOR | X-ray | T = 1 VLP (S37P) | |
| 6RRS | Cryo-EM | T = 3 VLP | |
| 6RRT | Cryo-EM | T = 4 VLP | |
| Qβ | 1QBE | X-ray | T = 3 VLP |
| 5KIP | Cryo-EM | T = 3 VLP | |
| 5VLY | Cryo-EM | T = 3 VLP | |
| 5VLZ | Cryo-EM | Mature virion, capsid and Mat (A2) | |
| 5VM7 | Cryo-EM | MurA-A2 complex | |
| 7LGE | Cryo-EM | T = 4 VLP | |
| 7LGF | Cryo-EM | Prolate VLP | |
| 7LGG | Cryo-EM | Oblate VLP | |
| 7LGH | Cryo-EM | Small prolate VLP | |
| 7LHD | Cryo-EM | Complete atomic model of Qβ | |
| 7TJD | X-ray | T = 1 VLP | |
| PP7 | 6N4V | Cryo-EM | T = 4 VLP |
| 2QUX | X-ray | CP/RNA complex | |
| 2QUD | X-ray | CP dimer | |
| 1DWN | X-ray | T = 3 VLP | |
| AP205 | 5JZR | NMR | CP dimer |
| 5FS4 | X-ray | CP dimer | |
| 5LQP | Cryo-EM | T = 3 VLP | |
| ΦCb5 | 2W4Z | X-ray | T = 3 VLP, from mature virions |
| 2W4Y | X-ray | T = 3 VLP, from overexpression of CP | |
| PRR1 | 2VF9 | X-ray | T = 3 VLP |
| 4ANG | X-ray | T = 3 VLP with RNA operator | |
| fr | 1FRS | X-ray | T = 3 VLP, WT |
| 1FR5 | X-ray | T = 3 VLP, 4 residue deletion in FG loop | |
| GA | 1GAV | X-ray | T = 3 VLP |
| Nonculturable, pre-2018, ssRNA phages | |||
| AVE002 | 6YF9 | X-ray | T = 3 VLP |
| AVE015 | 6YFA | X-ray | T = 3 VLP |
| AVE016 | 6YFB | X-ray | Prolate VLP |
| AVE019 | 6YFC | X-ray | T = 3 VLP |
| Beihai14 | 6YFD | X-ray | T = 3 VLP, unusual CP |
| Beihai19 | 6YFE | X-ray | T = 3 VLP |
| Beihai21 | 6YFF | X-ray | T = 3 VLP |
| Beihai32 | 6YFG | X-ray | T = 3 VLP |
| EMS014 | 6YFH | X-ray | T = 3 VLP |
| 6YFI | X-ray | CP dimer | |
| ESE001 | 6YFJ | X-ray | T = 3 VLP |
| ESE007 | 6YFK | X-ray | T = 3 VLP |
| ESE020 | 6YFL | X-ray | T = 3 VLP |
| ESE021 | 6YFM | X-ray | T = 3 VLP |
| ESE058 | 6YFN | X-ray | T = 3 VLP |
| NT-214 | 6YFQ | X-ray | T = 3 VLP |
| NT-391 | 6YFR | X-ray | T = 3 VLP |
| Wenzhou1 | 6YFT | X-ray | T = 3 VLP |
| Wenzhou4 | 6YFU | X-ray | T = 3 VLP |
| PQ-465 | 6YFS | X-ray | T = 3 VLP |
| AC | 6YF7 | X-ray | T = 3 VLP |
| GQ-112 | 6YFP | X-ray | T = 3 VLP |
| GQ-907 | 6YFO | X-ray | T = 3 VLP |