Table 1.
PDB entries discussed in this paper, grouped by molecule
| PDB ID | Method | Res. (Å) | Rel. datea | Molecule/title | Proteins | RNAs | Ligands (in v1.0) | Problem | Major rev.a | Ref. |
|---|---|---|---|---|---|---|---|---|---|---|
| 6nur | cryoEM | 3.10 | 05/29/19 | SARS-CoV RdRpb | Nsp12, Nsp8, Nsp7 | - | Zn | seq offset | - | (25) |
| 6nus | cryoEM | 3.50 | 05/29/19 | SARS-CoV RdRp | Nsp12, Nsp8, Nsp7 | - | Zn | seq offset | - | (25) |
| 6vyo | x-ray | 1.70 | 03/11/20 | nucleocapsid Pprot | 4 x RNA-bdg dom | - | Zn | Zn for Cl | 04/08/20 | - |
| v2.0 | x-ray | 1.70 | 04/15/20 | nucleocapsid Pprot | 4 x RNA-bdg dom | - | Zn, Cl | v2.0 OK | - | - |
| 6w41 | x-ray | 3.08 | 03/25/20 | spike/antibody | spike RBD, Fab | - | NAG, SO4 | bad SS, NAG | - | - |
| 6yLa | x-ray | 2.42 | 04/15/20 | spike/antibody | spike RBD, Fab | - | NAG | hi-res OK | - | - |
| 6w9c | x-ray | 2.70 | 04/01/20 | PL protease | 3 x protease | - | Zn, Cl | bad ZnFs | 05/06/20 | - |
| 6wrh | x-ray | 1.60 | 05/06/20 | PL protease | protease | - | Zn, Cl, PO4 | hi-res OK | - | - |
| 6m71 | cryoEM | 2.90 | 04/01/20 | RdRp | Nsp12, Nsp8, Nsp7 | - | - | seq offset | 05/27/20 | (23) |
| 7btf | cryoEM | 2.95 | 04/08/20 | RdRp complex | Nsp12, Nsp8, Nsp7 | - | Zn | seq offset | 05/27/20 | (23) |
| 7bv1 | cryoEM | 2.80 | 04/22/20 | RdRp apo complex | Nsp12, Nsp8, Nsp7 | - | Zn | seq offset | 05/27/20 | (26) |
| 7bv2 | cryoEM | 2.50 | 04/22/20 | RdRp/RNA/RTP | Nsp12, Nsp8, Nsp7 | 30, 20 | remdesivir, Zn, Mg, PPi | offset, RNA | 05/27/20 | (26) |
| 6yyt | cryoEM | 2.90 | 05/13/20 | RdRp/RNA product | Nsp12, Nsp8, Nsp7 | 4 × 18 | Zn | - | - | (24) |
| 7bzf | cryoEM | 3.26 | 06/03/20 | RdRp post-catalytic | Nsp12, Nsp8, Nsp7 | 31, 14 | Zn | - | - | (27) |
| 7c2k | cryoEM | 2.93 | 06/03/20 | RdRp pre-catalytic | Nsp12, Nsp8, Nsp7 | 29, 18 | Zn | - | - | (27) |
| 6xqb | cryoEM | 3.40 | 07/29/20 | RdRp/RNA | Nsp12 | 2 × 9 | Zn, Mg | seq offset | - | - |
| 7ctt | cryoEM | 3.20 | 10/02/20 | RpRp/favipiravir | Nsp12, Nsp8, Nsp7 | 40, 20 | favipiravir, Zn, Mg | - | - | (28) |
| 7aap | cryoEM | 2.60 | 10/23/20 | RpRp/favipiravir | Nsp12, Nsp8, Nsp7 | 30, 24 | favipiravir, Zn, Mg | - | - | - |
a
Dates compare release with revision dates; a major revision changes coordinates, sequence, or chemical identity and moves to the next integer version.
b
RdRp = RNA-dependent RNA polymerase. All structures are from SARS-CoV-2 except the first two.