Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8sq9
Q-score: 0.528
Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA
Mol Cell (2023) 83 pp. 3921-3930.e7 [ DOI: doi:10.1016/j.molcel.2023.10.001 Pubmed: 37890482 ]
- 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)
- Sars-cov-2 replication-transcription complex bound to nsp9 and umpcpp, as a pre-catalytic nmpylation intermediate (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Water (18 Da, Ligand)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine (482 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 rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Magnesium ion (24 Da, Ligand)
- Primer rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8sqj
Q-score: 0.511
Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA
Mol Cell (2023) 83 pp. 3921-3930.e7 [ DOI: doi:10.1016/j.molcel.2023.10.001 Pubmed: 37890482 ]
- Sars-cov-2 replication-transcription complex bound to rna-nsp9, as a noncatalytic rna-nsp9 binding mode (Complex from Severe acute respiratory syndrome coronavirus 2)
- 5'-o-[(r)-hydroxy(thiophosphonooxy)phosphoryl]guanosine (459 Da, Ligand)
- 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)
- Water (18 Da, Ligand)
- Primer rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- 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 rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Sars-cov-2 5' utr (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8sqk
Q-score: 0.533
Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA
Mol Cell (2023) 83 pp. 3921-3930.e7 [ DOI: doi:10.1016/j.molcel.2023.10.001 Pubmed: 37890482 ]
- 5'-o-[(r)-hydroxy(thiophosphonooxy)phosphoryl]guanosine (459 Da, Ligand)
- 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)
- Rna-directed rna polymerase nsp12 (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 5' utr (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Template rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 replication-transcription complex bound to rna-nsp9 and gdp-betas, as a pre-catalytic dernaylation/mrna capping intermediate (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7uo4
Q-score: 0.457
Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Gotte M, Chait BT, Campbell EA, Darst SA
Nature (2023) 614 pp. 781-787 [ DOI: doi:10.1038/s41586-022-05664-3 Pubmed: 36725929 ]
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Sars-cov-2 replication-transcription complex (Complex from Severe acute respiratory syndrome coronavirus 2)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Water (18 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]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (531 Da, Ligand)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 replication-transcription complex bound to ATP, in a pre-catalytic state
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7uo7
Q-score: 0.451
Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Gotte M, Chait BT, Campbell EA, Darst SA
Nature (2023) 614 pp. 781-787 [ Pubmed: 36725929 DOI: doi:10.1038/s41586-022-05664-3 ]
- Magnesium ion (24 Da, Ligand)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- 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)
- Zinc ion (65 Da, Ligand)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 replication-transcription complex + atp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Adenosine-5'-triphosphate (507 Da, Ligand)
SARS-CoV-2 replication-transcription complex bound to UTP, in a pre-catalytic state.
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 7uo9
Q-score: 0.487
Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Gotte M, Chait BT, Campbell EA, Darst SA
Nature (2023) 614 pp. 781-787 [ Pubmed: 36725929 DOI: doi:10.1038/s41586-022-05664-3 ]
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 replication-transcription complex + utp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Uridine 5'-triphosphate (484 Da, Ligand)
- Water (18 Da, Ligand)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 replication-transcription complex bound to GTP, in a pre-catalytic state
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 7uob
Q-score: 0.548
Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Gotte M, Chait BT, Campbell EA, Darst SA
Nature (2023) 614 pp. 781-787 [ Pubmed: 36725929 DOI: doi:10.1038/s41586-022-05664-3 ]
- 3'-deoxyuridine-5'-monophosphate (308 Da, Ligand)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- 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)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Sars-cov-2 replication-transcription complex + gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 replication-transcription complex bound to CTP, in a pre-catalytic state
Resolution: 2.67 Å
EM Method: Single-particle
Fitted PDBs: 7uoe
Q-score: 0.523
Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Gotte M, Chait BT, Campbell EA, Darst SA
Nature (2023) 614 pp. 781-787 [ DOI: doi:10.1038/s41586-022-05664-3 Pubmed: 36725929 ]
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Sars-cov-2 replication-transcription complex + ctp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 3'-deoxyuridine-5'-monophosphate (308 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 7thm
Q-score: 0.486
Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawlowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS
Nature (2022) 609 pp. 793-800 [ DOI: doi:10.1038/s41586-022-05185-z Pubmed: 35944563 ]
- Manganese (ii) ion (54 Da, Ligand)
- Pyrophosphate 2- (175 Da, Ligand)
- 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)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 replication-transcription complex with a native n-terminus nsp9 bound to niran domain of nsp12. (172 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - engaged class
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7rdy
Q-score: 0.472
Chen J, Wang Q, Malone B, Llewellyn E, Pechersky Y, Maruthi K, Eng ET, Perry JK, Campbell EA, Shaw DE, Darst SA
Nat Struct Mol Biol (2022) 29 pp. 250-260 [ DOI: doi:10.1038/s41594-022-00734-6 Pubmed: 35260847 ]
- Product rna (11 kDa, RNA from synthetic construct)
- Sars-cov-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-rtc - engaged class (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template rna (17 kDa, RNA from synthetic construct)
- Chapso (631 Da, Ligand)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Aluminum fluoride (83 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Helicase (67 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)