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Porcine epidemic diarrhea virus complete core polymerase complex
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 ]
- Nsp12 (108 kDa, Protein from Porcine epidemic diarrhea virus)
- Nsp7 (9 kDa, Protein from Porcine epidemic diarrhea virus)
- Nsp8 (21 kDa, Protein from Porcine epidemic diarrhea virus)
- Rna (55-mer) (17 kDa, RNA from synthetic construct)
- Rna (33-mer) (10 kDa, RNA from synthetic construct)
- 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)
- Zinc ion (65 Da, Ligand)
Structure of SARS-CoV-2 RNA-dependent RNA polymerase with gossypol binding
To Be Published
- Gossypol (518 Da, Ligand)
- Sars-cov-2 nsp12-nsp7-nsp8 complex bound to gossypol (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 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)
Porcine epidemic diarrhea virus core polymerase complex
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 ]
- Nsp7 (6 kDa, Protein from Porcine epidemic diarrhea virus)
- Nsp8 (12 kDa, Protein from Porcine epidemic diarrhea virus)
- Nsp12 (104 kDa, Protein 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)
- 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)
- Zinc ion (65 Da, Ligand)
A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase
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 [ Pubmed: 35110538 DOI: doi:10.1038/s41467-022-28113-1 ]
- 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)
- Magnesium ion (24 Da, Ligand)
- Nsp12-nsp7-nsp8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- [[(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)
- Rna (Complex)
- Rna-directed rna polymerase (109 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Nsp12-nsp7-nsp8-rna-at9010 (160 kDa, Complex)
Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase
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 ]
- Sars-cov-2 nsp7 (9 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)
- 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 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Zinc ion (65 Da, Ligand)
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 ]
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -3. (Complex)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*g)-d(p*(rmp))-r(p*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and nsp8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*gp*cp*ap*up*cp*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
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 ]
- Rna (5'-r(p*up*cp*ap*cp*up*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 complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -4. (Complex)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*a)-d(p*(rmp))-r(p*gp*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7b3d
Q-score: 0.558
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 ]
- Sars-cov-2 nsp7 (9 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)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing amp at position -4. (Complex)
- Sars-cov-2 rna-dependent rna polymerase nsp12 (Complex from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Zinc ion (65 Da, Ligand)
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 [ DOI: doi:10.1016/j.cell.2020.11.016 Pubmed: 33232691 ]
- Primer (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 extended rtc (Complex)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp7, nsp8, nsp9, nsp12 and nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Template (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Architecture of a SARS-CoV-2 mini replication and transcription complex
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 [ Pubmed: 33208736 DOI: doi:10.1038/s41467-020-19770-1 ]
- Rna (25-mer) (8 kDa, RNA 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)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein 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)
- Nsp12-nsp7-nsp8-nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)