Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8tom
Q-score: 0.253
Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA
Nat Struct Mol Biol (2024) 31 pp. 1778-1788 [ DOI: doi:10.1038/s41594-024-01349-9 Pubmed: 38951624 ]
- Zinc ion (65 Da, Ligand)
- Escherichia coli rna polymerase closed complex intermediate at the lambda pr promoter (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Chapso (631 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 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Escherichia coli sigma 70 rna polymerase bound to lambda pr promoter dna (Complex)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Template strand of lambda pr promoter dna (27 kDa, DNA from Escherichia virus Lambda)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- Lambda pr promoter dna (Complex from Escherichia virus Lambda)
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lambda pr promoter dna (27 kDa, DNA from Escherichia virus Lambda)
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 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Nontemplate strand of lambda pr dna promoter (27 kDa, DNA from Escherichia virus Lambda)
- Template strand of lambda pr dna promoter (27 kDa, DNA 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)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- Lambda pr promoter dna (class 2) (Complex from Escherichia virus Lambda)
- Escherichia coli rna polymerase bound to lambda pr promoter dna (Complex)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 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 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Lambda pr (-5g to c) promoter dna (Complex from Escherichia virus Lambda)
- Zinc ion (65 Da, Ligand)
- Nontemplate strand of lambda pr dna promoter (-5g to c) (27 kDa, DNA 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)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Template strand of lambda pr promoter dna (-5c to g) (27 kDa, DNA from Escherichia virus Lambda)
- Chapso (631 Da, Ligand)
- Escherichia coli rna polymerase bound to lambda pr promoter dna (-5g to c) (Complex)
Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6psq
Q-score: 0.479
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpc (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6psr
Q-score: 0.48
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpi1 (Complex from Escherichia coli)
- Chapso (631 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6pss
Q-score: 0.446
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Zinc ion (65 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA 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)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and mutant rpst p2 as trpi1.5a (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 beta' (158 kDa, Protein from Escherichia coli)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6pst
Q-score: 0.514
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA 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)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli sigma70-holoenzyme bound to trar and mutant rpst p2 as trpi1.5b (Complex from Escherichia coli)
- Chapso (631 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6psu
Q-score: 0.426
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Chapso (631 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpi2 (Complex from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6psv
Q-score: 0.468
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Zinc ion (65 Da, Ligand)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as tprerpo (Complex 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)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)