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: 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 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]

Sample:

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)
Guanosine-5'-triphosphate (523 Da, Ligand)
Rna (27-mer) (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Water (18 Da, Ligand)
Non-structural protein 9 (12 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)
E-rtc_smp-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 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-34308

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

Release date: Dec. 7, 2022
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 ]

Sample:

E-rtc_rna-nsp9 (Complex 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)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (5'-r(p*ap*u)-3') (590 Da, RNA from Severe acute respiratory syndrome coronavirus 2)
Water (18 Da, Ligand)
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)
Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 9 (12 kDa, Protein 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-34318

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

Release date: Nov. 30, 2022
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 ]

Sample:

Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 (25-mer) (8 kDa, RNA from synthetic construct)
Rna (Complex)
Replicase polyprotein (Complex)
Non-structural protein 9 (12 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)
Uridine-5'-monophosphate (324 Da, Ligand)
Template (10 kDa, RNA from synthetic construct)

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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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EMD-30504

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Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis

Release date: Dec. 9, 2020
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 [ Pubmed: 33232691 DOI: doi:10.1016/j.cell.2020.11.016 ]

Sample:

Sars-cov-2 extended rtc (Complex)
Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Guanosine-5'-diphosphate (443 Da, Ligand)
Rna (Complex 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 (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Template (18 kDa, RNA 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)
Nsp7, nsp8, nsp9, nsp12 and nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-30492

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Architecture of a SARS-CoV-2 mini replication and transcription complex

Release date: Nov. 4, 2020
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7cxm
Q-score: 0.461

Yan L, Zhang Y, Ge J, Zheng L, Gao Y, Wang T, Jia Z, Wang H, Huang Y, Li M, Wang Q, Rao Z, Lou Z

Nat Commun (2020) 11 pp. 5874-5874 [ DOI: doi:10.1038/s41467-020-19770-1 Pubmed: 33208736 ]

Sample:

Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Nsp12-nsp7-nsp8-nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
Nsp12-nsp7-nsp8-nsp13-rna (Complex)
Rna (5'-r(p*up*up*up*up*up*u)-3') (1 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (26-mer) (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-30493

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Architecture of a SARS-CoV-2 mini replication and transcription complex

Release date: Nov. 4, 2020
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 7cxn
Q-score: 0.367

Yan L, Zhang Y, Ge J, Zheng L, Gao Y, Wang T, Jia Z, Wang H, Huang Y, Li M, Wang Q, Rao Z, Lou Z

Nat Commun (2020) 11 pp. 5874-5874 [ DOI: doi:10.1038/s41467-020-19770-1 Pubmed: 33208736 ]

Sample:

Template rna (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Nsp7, nsp8, nsp12, nsp13 and rna (Complex)
Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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)
Rna (5'-r(p*up*up*up*up*up*u)-3') (1 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Nsp7, nsp8, nsp12, nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
Primer rna (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)

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EMD-30252

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COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex

Release date: June 3, 2020
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 ]

Sample:

Structure of covid-19 rna-dependent rna polymerase in complex with rna (155 kDa, Complex 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)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (31-mer) (10 kDa, RNA from Foot-and-mouth disease virus)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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