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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8gwe
Q-score: 0.019
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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*ap*up*up*a)-3') (1 kDa, RNA 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)
- Replicase polyprotein 1a (8 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rna-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Helicase nsp13 (65 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Nsp (Complex)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rna-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Rna (Complex)
- Zinc ion (65 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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Protein from sars-cov-2 (Complex)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_smp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Rna (Complex)
- Zinc ion (65 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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- 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)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- E-rtc_smp-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Rna (27-mer) (10 kDa, RNA 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: 3.38 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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- 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)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- E-rtc_atmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Rna (5'-r(p*ap*u)-3') (590 Da, RNA from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Manganese (ii) ion (54 Da, Ligand)
- E-rtc_rna-nsp9 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- 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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Replicase polyprotein (Complex)
- Rna (25-mer) (8 kDa, RNA from synthetic construct)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Template (10 kDa, RNA from synthetic construct)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Zinc ion (65 Da, Ligand)
- E-rtc_ump-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
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 [ Pubmed: 34143953 DOI: doi:10.1016/j.cell.2021.05.033 ]
- Nsp 7, 8, 9, 10, 12, 13, 14 (Complex 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)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Mcap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 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)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Primer rna, template rna (Complex)
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 ]
- Primer rna, template rna (Complex)
- Magnesium ion (24 Da, Ligand)
- 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)
- Template rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 7cyq
Q-score: 0.384
Yan L, Ge J, Zheng L, Zhang Y, Gao Y, Wang T, Huang Y, Yang Y, Gao S, Li M, Liu Z, Wang H, Li Y, Chen Y, Guddat LW, Wang Q, Rao Z, Lou Z
Cell (2021) 184 pp. 184-193.e10 [ DOI: doi:10.1016/j.cell.2020.11.016 Pubmed: 33232691 ]
- Primer (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 extended rtc (Complex)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp7, nsp8, nsp9, nsp12 and nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Template (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)