Electron Microscopy Data Bank

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Porcine epidemic diarrhea virus complete core polymerase complex

Release date: Nov. 15, 2023
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8urb
Q-score: 0.49

Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN

bioRxiv (2023) [ DOI: doi:10.1101/2023.03.15.532841 Pubmed: 36993498 ]

Sample:

Core polymerase complex of the porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short rna substrate (185 kDa, Complex from Porcine epidemic diarrhea virus)
Nsp8 (21 kDa, Protein from Porcine epidemic diarrhea virus)
Rna (55-mer) (17 kDa, RNA from synthetic construct)
Zinc ion (65 Da, Ligand)
Nsp7 (9 kDa, Protein from Porcine epidemic diarrhea virus)
Nsp12 (108 kDa, Protein from Porcine epidemic diarrhea virus)
Rna (33-mer) (10 kDa, RNA from synthetic construct)

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EMD-34370

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Structure of SARS-CoV-2 RNA-dependent RNA polymerase with gossypol binding

Release date: Nov. 1, 2023
EM Method: Tomography
Fitted PDBs: 8gy6
Q-score: 0.318

Wang W, Li W, Ren M, Li F

To Be Published

Sample:

Sars-cov-2 nsp12-nsp7-nsp8 complex bound to gossypol (Complex 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)
Gossypol (518 Da, Ligand)
Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)

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EMD-28162

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SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction

Release date: April 26, 2023
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8eir
Q-score: 0.602

Narwal M, Armache JP, Edwards TJ, Murakami KS

J Biol Chem (2023) 299 pp. 104697-104697 [ DOI: doi:10.1016/j.jbc.2023.104697 Pubmed: 37044215 ]

Sample:

EMD-29779

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Porcine epidemic diarrhea virus core polymerase complex

Release date: March 29, 2023
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8g6r
Q-score: 0.435

Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN

bioRxiv (2023) [ DOI: doi:10.1101/2023.03.15.532841 Pubmed: 36993498 ]

Sample:

Nsp7 (6 kDa, Protein from Porcine epidemic diarrhea virus)
Nsp12 (104 kDa, Protein from Porcine epidemic diarrhea virus)
Nsp8 (12 kDa, Protein from Porcine epidemic diarrhea virus)
Zinc ion (65 Da, Ligand)
Core replication complex of porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short rna substrate (185 kDa, Complex from Porcine epidemic diarrhea virus)
Rna (5'-r(p*gp*gp*up*up*gp*up*gp*ap*up*up*up*up*ap*ap*up*ap*gp*cp*up*u)-3') (6 kDa, RNA from synthetic construct)
Rna (5'-r(p*ap*ap*gp*ap*ap*gp*cp*up*ap*up*up*ap*ap*ap*ap*up*cp*ap*cp*a)-3') (6 kDa, RNA from synthetic construct)

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EMD-31061

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A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase

Release date: Feb. 16, 2022
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7ed5
Q-score: 0.522

Shannon A, Fattorini V, Sama B, Selisko B, Feracci M, Falcou C, Gauffre P, El Kazzi P, Delpal A, Decroly E, Alvarez K, Eydoux C, Guillemot JC, Moussa A, Good SS, La Colla P, Lin K, Sommadossi JP, Zhu Y, Yan X, Shi H, Ferron F, Canard B

Nat Commun (2022) 13 pp. 621-621 [ DOI: doi:10.1038/s41467-022-28113-1 Pubmed: 35110538 ]

Sample:

Nsp12-nsp7-nsp8 (Complex from Severe acute respiratory syndrome coronavirus 2)
[[(2r,3r,4r,5r)-5-(2-azanyl-6-oxidanylidene-1h-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (539 Da, Ligand)
Nsp12-nsp7-nsp8-rna-at9010 (160 kDa, Complex)
Rna-directed rna polymerase (109 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Non-structural protein 7 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (Complex)
Magnesium ion (24 Da, Ligand)
Zinc ion (65 Da, Ligand)
Rna (5'-r(p*cp*cp*cp*cp*ap*up*ap*ap*cp*up*up*ap*ap*up*cp*up*cp*ap*cp*ap*up*ap*gp*c)-3') (9 kDa, RNA from synthetic construct)
Non-structural protein 8 (24 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (5'-r(p*gp*cp*up*ap*up*gp*up*gp*ap*gp*ap*up*up*ap*ap*gp*up*up*ap*u*(at9))-3') (6 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-13116

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Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase

Release date: Aug. 25, 2021
Resolution: 5.5 Å
EM Method: Single-particle
Fitted PDBs: 7oyg
Q-score: 0.151

Jochheim FA, Tegunov D, Hillen HS, Schmitzova J, Kokic G, Dienemann C, Cramer P

Communications Biology (2021) 4 pp. 999- [ DOI: doi:10.1038/s42003-021-02529-9 ]

Sample:

Dimeric form of sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) (Complex from Severe acute respiratory syndrome coronavirus 2)
Sars-cov-2 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Sars-cov-2 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Rna (5'-r(p*up*gp*cp*ap*cp*up*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Sars-cov-2 rna-dependent rna polymerase (nsp12) (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Zinc ion (65 Da, Ligand)
Rna (5'-r(p*cp*up*ap*cp*gp*cp*ap*gp*up*g)-3') (4 kDa, RNA 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-11993

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Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with Remdesivir at position -3 (structure 1)

Release date: Dec. 23, 2020
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7b3b
Q-score: 0.501

Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P

Nat Commun (2021) 12 pp. 279-279 [ DOI: doi:10.1038/s41467-020-20542-0 Pubmed: 33436624 ]

Sample:

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EMD-11994

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Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with Remdesivir at position -4 (structure 2)

Release date: Dec. 23, 2020
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7b3c
Q-score: 0.455

Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P

Nat Commun (2021) 12 pp. 279-279 [ DOI: doi:10.1038/s41467-020-20542-0 Pubmed: 33436624 ]

Sample:

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