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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)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Magnesium ion (24 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)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 replication-transcription complex (Complex 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 ]
- 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)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Magnesium ion (24 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)
- Zinc ion (65 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 ]
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Sars-cov-2 replication-transcription complex + utp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Magnesium ion (24 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)
- Uridine 5'-triphosphate (484 Da, Ligand)
- Zinc ion (65 Da, Ligand)
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 ]
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 3'-deoxyuridine-5'-monophosphate (308 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)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 replication-transcription complex + gtp (Complex 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 [ Pubmed: 36725929 DOI: doi:10.1038/s41586-022-05664-3 ]
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (55-mer) (17 kDa, RNA from synthetic construct)
- Product rna (35-mer) (11 kDa, RNA from synthetic construct)
- Water (18 Da, Ligand)
- Sars-cov-2 replication-transcription complex + ctp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- 3'-deoxyuridine-5'-monophosphate (308 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)
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of HK022 putRNA-associated E.coli RNA polymerase elongation complex
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 7xue
Q-score: 0.476
Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY
Nat Commun (2022) 13 pp. 4668-4668 [ Pubmed: 35970830 DOI: doi:10.1038/s41467-022-32315-y ]
- Non-template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli (strain K12))
- Rna (nun gene and immunity region) (30 kDa, RNA from Shamshuipovirus HK022)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Hk022 putrna-associated e.coli rna polymerase elongation complex (440 kDa, Complex)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Rna polymerase (Complex from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna/rna (Complex)
cryo-EM structure of HK022 putRNA-less E.coli RNA polymerase elongation complex
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 7xug
Q-score: 0.446
Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY
Nat Commun (2022) 13 pp. 4668-4668 [ Pubmed: 35970830 DOI: doi:10.1038/s41467-022-32315-y ]
- Hk022 putrna-less e.coli rna polymerase elongation complex (440 kDa, Complex)
- Non-template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli (strain K12))
- Rna (nun gene and immunity region) (30 kDa, RNA from Shamshuipovirus HK022)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- E.coli rna polymerase (Complex from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna/rna (Complex)
Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elongation complex
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 7xui
Q-score: 0.416
Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY
Nat Commun (2022) 13 pp. 4668-4668 [ Pubmed: 35970830 DOI: doi:10.1038/s41467-022-32315-y ]
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Sigma70 bound hk022 putrna-associated e.coli rna polymerase elongation complex (510 kDa, Complex)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Rna polymerase (Complex from Escherichia coli (strain K12))
- Template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Rna (122-mer) (39 kDa, RNA from Shamshuipovirus HK022)
- Zinc ion (65 Da, Ligand)
- Dna/rna (Complex)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
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 [ Pubmed: 33883267 DOI: doi:10.1073/pnas.2102516118 ]
- Chapso (631 Da, Ligand)
- Rna (43-mer) (17 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Aluminum fluoride (83 Da, Ligand)
- Non-structural protein 8 (22 kDa, Protein 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)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (67 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (37-mer) (12 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
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 [ Pubmed: 33883267 DOI: doi:10.1073/pnas.2102516118 ]
- Chapso (631 Da, Ligand)
- Rna (43-mer) (17 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Aluminum fluoride (83 Da, Ligand)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (67 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)
- Rna (37-mer) (12 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)