SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 8gwk
Q-score: 0.423
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 ]
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Water (18 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- [(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)
- Magnesium ion (24 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)
SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8gwm
Q-score: 0.41
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 ]
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_mmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (26-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) (420 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)
- Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 8gw1
Q-score: 0.332
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)
- Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Manganese (ii) ion (54 Da, Ligand)
- Replicase polyprotein 1ab (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- E-rtc_ump-nsp9 (350 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
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 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Water (18 Da, Ligand)
- 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)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- E-rtc_rna-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Helicase nsp13 (65 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)
- 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)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Replicase polyprotein 1a (8 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: 3.39 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 ]
- Rna (Complex)
- Water (18 Da, Ligand)
- Primer (8 kDa, RNA 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 Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Helicase (66 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)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rna-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Nsp (Complex)
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 ]
- Rna (Complex)
- Water (18 Da, Ligand)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Protein from sars-cov-2 (Complex)
- 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)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 9 (12 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: 3.18 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 ]
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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 (27-mer) (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 9 (12 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: 3.38 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 ]
- 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)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 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_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)
- 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)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*ap*u)-3') (590 Da, RNA from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rna-nsp9 (Complex 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 Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Manganese (ii) ion (54 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 9 (12 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: 3.8 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 ]
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Replicase polyprotein (Complex)
- Zinc ion (65 Da, Ligand)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Template (10 kDa, RNA from synthetic construct)
- E-rtc_ump-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (25-mer) (8 kDa, RNA from synthetic construct)