Electron Microscopy Data Bank

Download Map 3D View

SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP

Release date: Feb. 28, 2024
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 ]

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)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Magnesium ion (24 Da, Ligand)
[(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)
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)
Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
E-rtc_rmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)

[Show more]

EMD-34302

Download Map 3D View

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

Release date: Oct. 25, 2023
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 ]

Sample:

Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
E-rtc_ump-nsp9 (350 kDa, 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)
Uridine-5'-monophosphate (324 Da, Ligand)
Water (18 Da, Ligand)
Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Replicase polyprotein 1ab (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)

[Show more]

EMD-34310

Download Map 3D View

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

Release date: Jan. 11, 2023
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 ]

Sample:

Replicase polyprotein 1a (8 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)
Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
E-rtc_rna-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 8 (21 kDa, Protein 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)
Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Zinc ion (65 Da, Ligand)
Helicase nsp13 (65 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)

[Show more]

EMD-34311

Download Map 3D View

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)

[Show more]

EMD-34312

Download Map 3D View

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)

[Show more]

EMD-34313

Download Map 3D View

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)

[Show more]

EMD-34317

Download Map 3D View

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)

[Show more]

EMD-34308

Download Map 3D View

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)

[Show more]

EMD-31146

Download Map 3D View

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)

[Show more]

EMD-31138

Download Map 3D View

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)

[Show more]

Filter By

Filter By