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))
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)
Cryo-EM structure of SoxS-dependent transcription activation complex with fpr promoter DNA
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7w5y
Q-score: 0.369
Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W
Nucleic Acids Res (2022) 50 pp. 11359-11373 [ Pubmed: 36243985 DOI: doi:10.1093/nar/gkac898 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Fpr promoter dna reverse strand (26 kDa, DNA from Escherichia coli)
- Fpr promoter dna forward strand (26 kDa, DNA from Escherichia coli)
- Dna (Complex)
- Soxs-dependent transcription activation complex with fpr promoter dna (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Regulatory protein soxs (12 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
Transcription antitermination complex: "pre-engaged" Qlambda-loading complex
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 7ubm
Q-score: 0.461
Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH
PNAS (2022) 119 pp. e2205278119-e2205278119 [ DOI: doi:10.1073/pnas.2205278119 Pubmed: 35951650 ]
- Antitermination protein q (22 kDa, Protein from Escherichia phage Lambda)
- Rna polymerase sigma factor rpod (71 kDa, Protein from Escherichia coli)
- Rna (5'-r(*up*gp*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (3 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Dna (53-mer) (18 kDa, DNA from Escherichia coli)
- Dna (52-mer) (18 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Transcription antitermination complex: "pre-engaged" qlambda-loading complex (500 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)
Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 7ubn
Q-score: 0.435
Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH
PNAS (2022) 119 pp. e2205278119-e2205278119 [ Pubmed: 35951650 DOI: doi:10.1073/pnas.2205278119 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Antitermination protein (22 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription termination/antitermination protein nusa (57 kDa, Protein from Escherichia coli)
- Dna (53-mer) (18 kDa, DNA from Escherichia phage Lambda)
- Dna (52-mer) (18 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Rna (5'-r(*up*gp*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (3 kDa, RNA from Escherichia coli)
- Transcription antitermination complex: nusa-containing "engaged" qlambda-loading complex (550 kDa, Complex from Escherichia coli)
- Rna polymerase sigma factor rpod (71 kDa, Protein from Escherichia coli)
Escherichia coli sigma 70-dependent paused transcription elongation complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7n4e
Q-score: 0.343
Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE
PNAS (2022) 119 pp. e2201301119-e2201301119 [ DOI: doi:10.1073/pnas.2201301119 Pubmed: 35653571 ]
- Dna (61-mer) (18 kDa, DNA from synthetic construct)
- Escherichia coli sigma 70-dependent paused transcription elongation complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 5'-r(*up*up*cp*gp*gp*ap*gp*ap*gp*gp*up*a)-3' (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna (61-mer) (18 kDa, DNA from synthetic construct)
- 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)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation
Resolution: 4.57 Å
EM Method: Single-particle
Fitted PDBs: 7vwy
Q-score: 0.359
Shi J, Wang F, Li F, Wang L, Xiong Y, Wen A, Jin Y, Jin S, Gao F, Feng Z, Li J, Zhang Y, Shang Z, Wang S, Feng Y, Lin W
Nucleic Acids Res (2022) 50 pp. 5974-5987 [ DOI: doi:10.1093/nar/gkac433 Pubmed: 35641097 ]
- Micf promoter dna scaffold forward strand (21 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Rob-dependent transcription activation complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Micf promoter dna scaffold reverse strand (21 kDa, DNA from Escherichia coli)
- Right origin-binding protein (33 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
A refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 7dy6
Q-score: 0.474
Wang F, Feng Y, Shang Z, Lin W
Biochem Biophys Res Commun (2021) 583 pp. 86-92 [ Pubmed: 34735884 DOI: doi:10.1016/j.bbrc.2021.10.048 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna (63-mer) (19 kDa, DNA from Escherichia coli)
- An escherichia coli rnap-promoter open complex (rpo) with sspa (Cell from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Stringent starvation protein a (24 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- 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))
- Dna (63-mer) (19 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
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 [ Pubmed: 34599106 DOI: doi:10.1073/pnas.2112877118 ]
- Rna polymerase (Complex from Escherichia coli)
- 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' (155 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Template strand of lambda pr promoter dna (27 kDa, DNA from Escherichia virus Lambda)
- Escherichia coli sigma 70 rna polymerase bound to lambda pr promoter dna (Complex)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein 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 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 [ Pubmed: 34599106 DOI: doi:10.1073/pnas.2112877118 ]
- Rna polymerase (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein 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)
- 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)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein 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)