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 [ Pubmed: 37890482 DOI: doi:10.1016/j.molcel.2023.10.001 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Sars-cov-2 5' utr (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Zinc ion (65 Da, Ligand)
- 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 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Primer rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 [ Pubmed: 37890482 DOI: doi:10.1016/j.molcel.2023.10.001 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Sars-cov-2 5' utr (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Primer rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Zinc ion (65 Da, Ligand)
- Template rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- 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 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein 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 [ Pubmed: 36725929 DOI: doi:10.1038/s41586-022-05664-3 ]
- [[(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)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Product rna (35-mer) (11 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 (Complex 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 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)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Sars-cov-2 replication-transcription complex + atp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (10 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 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 ]
- Sars-cov-2 replication-transcription complex + utp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Uridine 5'-triphosphate (484 Da, Ligand)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 backtracked complex bound to nsp13 helicase - nsp13(1)-BTC
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7krn
Q-score: 0.476
Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2102516118 Pubmed: 33883267 ]
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna (37-mer) (12 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 backtracked complex bound to nsp13 helicase - nsp13(1)-btc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Chapso (631 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (67 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Aluminum fluoride (83 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (43-mer) (17 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 backtracked complex complex bound to nsp13 helicase - nsp13(2)-BTC
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7kro
Q-score: 0.416
Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2102516118 Pubmed: 33883267 ]
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna (37-mer) (12 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Chapso (631 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 backtracked complex complex bound to nsp13 helicase - nsp13(2)-btc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Helicase (67 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Aluminum fluoride (83 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (43-mer) (17 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Structure of SARS-CoV-2 backtracked complex complex bound to nsp13 helicase - BTC (local refinement)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7krp
Q-score: 0.361
Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2102516118 Pubmed: 33883267 ]
- Rna (36-mer) (17 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna (37-mer) (12 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Chapso (631 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 backtracked complex complex bound to nsp13 helicase - btc (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Mfd-bound E.coli RNA polymerase elongation complex - I state
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6x2n
Q-score: 0.368
Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA
eLife (2021) 10 [ DOI: doi:10.7554/eLife.62117 Pubmed: 33480355 ]
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Rna (20-mer) (6 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Escherichia coli mfd-rna polymerase elongation complex: i state (570 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Transcription-repair-coupling factor (130 kDa, Protein from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
Mfd-bound E.coli RNA polymerase elongation complex - II state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6x43
Q-score: 0.476
Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA
eLife (2021) 10 [ DOI: doi:10.7554/eLife.62117 Pubmed: 33480355 ]
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Escherichia coli mfd-rna polymerase elongation complex: state ii (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna (20-mer) (6 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Transcription-repair-coupling factor (130 kDa, Protein from Escherichia coli)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli)