Structure of COVID-19 RNA-dependent RNA polymerase bound to penciclovir.
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7doi
Q-score: 0.599
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H
To Be Published
- Covid-19 rdrp complex bound to penciclovir (Complex from Severe acute respiratory syndrome coronavirus 2)
- Pyrophosphate 2- (175 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*cp*cp*up*ap*up*ap*ap*cp*up*up*ap*ap*up*cp*u)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- [(2r)-4-(2-azanyl-6-oxidanylidene-3h-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate (333 Da, Ligand)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*ap*gp*ap*up*up*ap*ap*gp*up*up*ap*u)-3') (3 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 7dok
Q-score: 0.554
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H
To Be Published
- Covid-19 rdrp complex (exntended conformation) bound to penciclovir (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*gp*cp*up*ap*up*gp*up*gp*ap*gp*ap*up*up*ap*ap*gp*up*up*ap*u)-3') (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Pyrophosphate 2- (175 Da, Ligand)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*cp*cp*cp*up*ap*up*ap*ap*cp*up*up*ap*ap*up*cp*up*cp*ap*cp*ap*up*ap*gp*c)-3') (7 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- [(2r)-4-(2-azanyl-6-oxidanylidene-3h-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate (333 Da, Ligand)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Structure of COVID-19 RNA-dependent RNA polymerase bound to favipiravir
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7dfg
Q-score: 0.598
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H
To Be Published
- Covid-19 rdrp complex bound to favipiravir (Complex from Severe acute respiratory syndrome coronavirus 2)
- Pyrophosphate 2- (175 Da, Ligand)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 6-fluoro-3-oxo-4-(5-o-phosphono-beta-d-ribofuranosyl)-3,4-dihydropyrazine-2-carboxamide (369 Da, Ligand)
- Rna (5'-r(p*cp*cp*cp*up*ap*up*ap*ap*cp*up*up*ap*ap*up*cp*u)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*ap*gp*ap*up*up*ap*ap*gp*up*up*ap*u)-3') (3 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Structure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 7dfh
Q-score: 0.535
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H
To Be Published
- Covid-19 rdrp complex bound to favipiravir (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*gp*cp*up*ap*up*gp*up*g*(lig))-3') (2 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Ribavirin monophosphate (324 Da, Ligand)
- Pyrophosphate 2- (175 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymeras (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*cp*cp*cp*cp*cp*ap*cp*ap*up*ap*gp*c)-3') (3 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Structure of COVID-19 RNA-dependent RNA polymerase bound to suramin
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 7d4f
Q-score: 0.608
Yin W, Luan X, Li Z, Zhou Z, Wang Q, Gao M, Wang X, Zhou F, Shi J, You E, Liu M, Wang Q, Jiang Y, Jiang H, Xiao G, Zhang L, Yu X, Zhang S, Eric Xu H
Nat Struct Mol Biol (2021) 28 pp. 319-325 [ Pubmed: 33674802 DOI: doi:10.1038/s41594-021-00570-0 ]
- Covid-19 rdrp complex bound to suramin (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 8-(3-(3-aminobenzamido)-4-methylbenzamido)naphthalene-1,3,5-trisulfonic acid (635 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the apo nsp12-nsp7-nsp8 complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7bv1
Q-score: 0.485
Yin W, Mao C, Luan X, Shen DD, Shen Q, Su H, Wang X, Zhou F, Zhao W, Gao M, Chang S, Xie YC, Tian G, Jiang HW, Tao SC, Shen J, Jiang Y, Jiang H, Xu Y, Zhang S, Zhang Y, Xu HE
Science (2020) 368 pp. 1499-1504 [ Pubmed: 32358203 DOI: doi:10.1126/science.abc1560 ]
- Rna-directed rna polymerase (109 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- The apo nsp12-nsp7-nsp8 complex (Complex from SARS bat coronavirus)
- Non-structural protein 8 (23 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7bv2
Q-score: 0.607
Yin W, Mao C, Luan X, Shen DD, Shen Q, Su H, Wang X, Zhou F, Zhao W, Gao M, Chang S, Xie YC, Tian G, Jiang HW, Tao SC, Shen J, Jiang Y, Jiang H, Xu Y, Zhang S, Zhang Y, Xu HE
Science (2020) 368 pp. 1499-1504 [ Pubmed: 32358203 DOI: doi:10.1126/science.abc1560 ]
- Rna-directed rna polymerase (109 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Pyrophosphate 2- (175 Da, Ligand)
- [(2~{r},3~{s},4~{r},5~{r})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (371 Da, Ligand)
- Water (18 Da, Ligand)
- Templete (9 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- The nsp12-nsp7-nsp8 complex bound to the template-primer rna and triphosphate form of remdesivir(rtp) (Complex from SARS bat coronavirus)
- Non-structural protein 8 (23 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)