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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 Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 1)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7mkd
Q-score: 0.495
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2112877118 Pubmed: 34599106 ]
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Template strand of lambda pr promoter dna (27 kDa, DNA from Escherichia virus Lambda)
- Nontemplate strand of lambda pr promoter dna (27 kDa, DNA from Escherichia virus Lambda)
- Lambda pr promoter dna (Complex from Escherichia virus Lambda)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Escherichia coli sigma 70 rna polymerase bound to lambda pr promoter dna (Complex)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 2)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7mke
Q-score: 0.412
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2112877118 Pubmed: 34599106 ]
- Template strand of lambda pr dna promoter (27 kDa, DNA from Escherichia virus Lambda)
- Escherichia coli rna polymerase bound to lambda pr promoter dna (Complex)
- Chapso (631 Da, Ligand)
- Lambda pr promoter dna (class 2) (Complex from Escherichia virus Lambda)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- Nontemplate strand of lambda pr dna promoter (27 kDa, DNA from Escherichia virus Lambda)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR (-5G to C) promoter DNA
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7mki
Q-score: 0.492
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2112877118 Pubmed: 34599106 ]
- Chapso (631 Da, Ligand)
- Lambda pr (-5g to c) promoter dna (Complex from Escherichia virus Lambda)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Nontemplate strand of lambda pr dna promoter (-5g to c) (27 kDa, DNA from Escherichia virus Lambda)
- Escherichia coli rna polymerase bound to lambda pr promoter dna (-5g to c) (Complex)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Template strand of lambda pr promoter dna (-5c to g) (27 kDa, DNA from Escherichia virus Lambda)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of Escherichia coli RNA polymerase bound to T7A1 promoter DNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7mkj
Q-score: 0.509
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2112877118 Pubmed: 34599106 ]
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- T7a1 promoter dna (Complex from Escherichia phage T7)
- Nontemplate strand of t7a1 promoter dna (28 kDa, DNA from Escherichia phage T7)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Template strand of t7a1 promoter dna (27 kDa, DNA from Escherichia phage T7)
- Escherichia coli rna polymerase bound to t7a1 promoter dna (Complex)
- Zinc ion (65 Da, Ligand)