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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8gwf
Q-score: 0.29
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- E-rtc_rna-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Nsp (Complex)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8gwg
Q-score: 0.007
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Water (18 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Protein from sars-cov-2 (Complex)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_smp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8gwi
Q-score: 0.185
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Water (18 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna (27-mer) (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_smp-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 8gwn
Q-score: 0.407
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- E-rtc_atmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 8gwb
Q-score: -0.011
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Water (18 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rna-nsp9 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*ap*u)-3') (590 Da, RNA from Severe acute respiratory syndrome coronavirus 2)
- Manganese (ii) ion (54 Da, Ligand)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8gwo
Q-score: 0.362
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from synthetic construct)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Replicase polyprotein (Complex)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (25-mer) (8 kDa, RNA from synthetic construct)
- E-rtc_ump-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Rna (Complex)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
SARS-CoV-2 RdRP catalytic complex with T33-1 RNA
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7dte
Q-score: 0.528
Wu J, Wang H, Liu Q, Li R, Gao Y, Fang X, Zhong Y, Wang M, Wang Q, Rao Z, Gong P
Cell Rep (2021) 37 pp. 109882-109882 [ DOI: doi:10.1016/j.celrep.2021.109882 Pubmed: 34653416 ]
- Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase catalytic complex (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (33-mer) (10 kDa, RNA from Foot-and-mouth disease virus)
- Sars-cov-2 rna-dependent rna polymerase (Complex)
- Rna (57-mer) (18 kDa, RNA from Foot-and-mouth disease virus)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Zinc ion (65 Da, Ligand)
Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2021) 184 pp. 3474-3485.e11 [ DOI: doi:10.1016/j.cell.2021.05.033 Pubmed: 34143953 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna, template rna (Complex)
- Mcap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7egq
Q-score: 0.384
Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2021) 184 pp. 3474-3485.e11 [ DOI: doi:10.1016/j.cell.2021.05.033 Pubmed: 34143953 ]
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Cap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Primer rna, template rna (Complex)
- Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 7bzf
Q-score: 0.47
Wang Q, Wu J, Wang H, Gao Y, Liu Q, Mu A, Ji W, Yan L, Zhu Y, Zhu C, Fang X, Yang X, Huang Y, Gao H, Liu F, Ge J, Sun Q, Yang X, Xu W, Liu Z, Yang H, Lou Z, Jiang B, Guddat LW, Gong P, Rao Z
Cell (2020) 182 pp. 417-428.e13 [ DOI: doi:10.1016/j.cell.2020.05.034 Pubmed: 32526208 ]
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (31-mer) (10 kDa, RNA from Foot-and-mouth disease virus)
- Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(*up*gp*up*up*cp*gp*ap*cp*gp*ap*cp*ap*cp*a)-3') (4 kDa, RNA from Foot-and-mouth disease virus)
- Structure of covid-19 rna-dependent rna polymerase in complex with rna (155 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)