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 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- (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)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase unwinding intermediate (i1a) at the lambda pr promoter (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
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 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase unwinding intermediate (i1d) at the lambda pr promoter (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- (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)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
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 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- 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 (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- (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)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
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 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase unwinding intermediate (i1c) at the lambda pr promoter (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
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 ]
- Template strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Nontemplate strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Escherichia coli rna polymerase closed complex intermediate at the lambda pr promoter (Complex from Escherichia coli)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8u3b
Q-score: 0.454
Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B
Nucleic Acids Res (2024) 52 pp. 1471-1482 [ DOI: doi:10.1093/nar/gkad1231 Pubmed: 38197271 ]
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna (69-mer) (21 kDa, DNA from Escherichia coli)
- E. coli narl transcription activation complex on the year promoter (625 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Nitrate/nitrite response regulator protein narl (8 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Rna (5'-d(*(gtp))-r(p*ap*a)-3') (1 kDa, RNA from Escherichia coli)
- Dna (69-mer) (21 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Structure of Escherichia coli CedA in complex with transcription initiation complex
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8ftd
Q-score: 0.456
Vasilyev N, Liu MMJ, Epshtein V, Shamovsky I, Nudler E
Nat Struct Mol Biol (2024) 31 pp. 141-149 [ DOI: doi:10.1038/s41594-023-01154-w Pubmed: 38177674 ]
- Rna polymerase sigma factor rpod (69 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Transcription unit ssra promoter template dna (26 kDa, DNA from Escherichia coli)
- Cell division activator ceda (9 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Transcription unit ssra promoter non-template dna (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Escherichia coli ceda in complex with initiation complex (520 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Cryo-EM structure of CII-dependent transcription activation complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8igr
Q-score: 0.52
Zhao M, Gao B, Wen A, Feng Y, Lu YQ
Structure (2023) 31 pp. 968- [ Pubmed: 37269829 DOI: doi:10.1016/j.str.2023.05.008 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Nontemplate strand dna (26 kDa, DNA from Escherichia coli (strain K12))
- Template strand dna (26 kDa, DNA from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Transcriptional activator ii (11 kDa, Protein from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Cii-dependent transcription activation complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
Cryo-EM structure of RNAP-promoter open complex at lambda promoter PRE
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8igs
Q-score: 0.469
Zhao M, Gao B, Wen A, Feng Y, Lu YQ
Structure (2023) 31 pp. 968- [ Pubmed: 37269829 DOI: doi:10.1016/j.str.2023.05.008 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Template strand dna (26 kDa, DNA from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Rnap-promoter open complex (Complex from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Non-template strand dna (26 kDa, DNA from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
The cryo-EM structure of C. crescentus GcrA-TACup
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7ye1
Q-score: 0.407
Nucleic Acids Res (2023) [ ]
- Dna (57-mer)-non template (17 kDa, DNA from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit omega (13 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna (57-mer)-template (17 kDa, DNA from Caulobacter vibrioides NA1000)
- Dna (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (154 kDa, Protein from Caulobacter vibrioides NA1000)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Caulobacter vibrioides NA1000)
- The cryo-em structure of c. crescentus gcra-tacup (Complex from Caulobacter vibrioides NA1000)
- Cell cycle regulatory protein gcra (18 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase subunit beta (151 kDa, Protein from Caulobacter vibrioides NA1000)
- Dna-directed rna polymerase/gcra/tacup (Complex)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Caulobacter vibrioides NA1000)