Escherichia coli RNA polymerase unwinding intermediate (I1a) at the lambda PR promoter
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8to1
Q-score: 0.477
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)
- 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))
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Escherichia coli rna polymerase unwinding intermediate (i1a) at the lambda pr promoter (Complex from Escherichia coli)
Escherichia coli RNA polymerase unwinding intermediate (I1d) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8to6
Q-score: 0.465
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)
- 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))
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Escherichia coli rna polymerase unwinding intermediate (i1d) at the lambda pr promoter (Complex from Escherichia coli)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
Escherichia coli RNA polymerase unwinding intermediate (I1b) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8to8
Q-score: 0.461
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)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- 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))
- 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))
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Escherichia coli rna polymerase unwinding intermediate (i1b) at the lambda pr promoter (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8toe
Q-score: 0.462
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)
- 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))
- Chapso (631 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli rna polymerase unwinding intermediate (i1c) at the lambda pr promoter (Complex from Escherichia coli)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
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)
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 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Template strand of t7a1 promoter dna (27 kDa, DNA from Escherichia phage T7)
- Zinc ion (65 Da, Ligand)
- T7a1 promoter dna (Complex from Escherichia phage T7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Escherichia coli rna polymerase bound to t7a1 promoter dna (Complex)
- 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)
- Nontemplate strand of t7a1 promoter dna (28 kDa, DNA from Escherichia phage T7)
- Rna polymerase (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)