Electron Microscopy Data Bank

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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

Release date: Jan. 11, 2023
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 ]

Sample:

E-rtc_rna-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Guanosine-5'-triphosphate (523 Da, Ligand)
Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Water (18 Da, Ligand)
Zinc ion (65 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)
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 (Complex)
Nsp (Complex)

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EMD-34312

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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

Release date: Dec. 14, 2022
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 ]

Sample:

Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Guanosine-5'-triphosphate (523 Da, Ligand)
Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Water (18 Da, Ligand)
Zinc ion (65 Da, Ligand)
Rna (Complex)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Protein from sars-cov-2 (Complex)
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)
Template (10 kDa, RNA 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)

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EMD-34313

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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

Release date: Dec. 14, 2022
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 ]

Sample:

Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Guanosine-5'-triphosphate (523 Da, Ligand)
Water (18 Da, Ligand)
Zinc ion (65 Da, Ligand)
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)
Primer (8 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 9 (12 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 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-34317

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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

Release date: Dec. 14, 2022
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 ]

Sample:

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)
E-rtc_atmp-nsp9_gmppnp (Complex 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 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)

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EMD-31146

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Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading

Release date: Sept. 22, 2021
EM Method: Single-particle
Fitted PDBs: 7eiz
Q-score: 0.333

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 ]

Sample:

Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Template (8 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 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Magnesium ion (24 Da, Ligand)
Primer rna, template rna (Complex)
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 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Mcap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-31138

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Co-transcriptional capping machineries in SARS-CoV-2 RTC: Coupling of N7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading

Release date: July 21, 2021
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 [ Pubmed: 34143953 DOI: doi:10.1016/j.cell.2021.05.033 ]

Sample:

Primer rna, template rna (Complex)
Proofreading exoribonuclease (59 kDa, Protein 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)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Primer rna (8 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 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Template rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Magnesium ion (24 Da, Ligand)
Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)

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