Cryo-EM structure of Escherichia coli paused complex of transcription termination (TTC-pause)
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 7yp9
Q-score: 0.345
You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y
Nature (2023) 613 pp. 783-789 [ DOI: doi:10.1038/s41586-022-05604-1 Pubmed: 36631609 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase (Complex)
- Dna/rna (Complex)
- E. coli paused complex of transcription termination (400 kDa, Complex from Escherichia coli K-12)
- Rna (5'-r(*gp*cp*gp*up*cp*gp*cp*ap*gp*gp*cp*cp*up*up*up*up*up*ap*up*u)-3') (6 kDa, RNA from synthetic construct)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 7ypa
Q-score: 0.509
You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y
Nature (2023) 613 pp. 783-789 [ DOI: doi:10.1038/s41586-022-05604-1 Pubmed: 36631609 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- E. coli hairpin-nucleation complex of transcription termination (400 kDa, Complex from Escherichia coli K-12)
- Dna-directed rna polymerase (Complex)
- Dna/rna (Complex)
- Rna (5'-r(*gp*cp*gp*up*cp*gp*cp*ap*gp*gp*cp*cp*up*up*up*up*up*ap*up*u)-3') (6 kDa, RNA from synthetic construct)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)
- Rna (5'-r(*cp*cp*up*gp*cp*gp*ap*cp*gp*c)-3') (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
Cryo-EM structure of Escherichia coli release complex of transcription termination (TTC-release)
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 7ypb
Q-score: 0.399
You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y
Nature (2023) 613 pp. 783-789 [ DOI: doi:10.1038/s41586-022-05604-1 Pubmed: 36631609 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Rna (5'-r(*gp*cp*gp*up*cp*gp*cp*ap*gp*gp*cp*cp*up*up*up*up*up*ap*up*u)-3') (6 kDa, RNA from synthetic construct)
- Rna (5'-r(*gp*gp*cp*cp*up*gp*cp*gp*ap*cp*gp*a)-3') (3 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase (Complex)
- Dna/rna (Complex)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- E. coli release complex of transcription termination (400 kDa, Complex from Escherichia coli K-12)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6c6s
Q-score: 0.426
Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA
Cell (2018) 173 pp. 1650-1662.e14 [ DOI: doi:10.1016/j.cell.2018.05.017 Pubmed: 29887376 ]
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna (29-mer) (9 kDa, DNA from Escherichia coli)
- E.coli rfah-elongation complex (412 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Rna (5'-r(*gp*cp*ap*up*up*cp*ap*ap*ap*gp*cp*cp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli)
CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6c6t
Q-score: 0.462
Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA
Cell (2018) 173 pp. 1650-1662.e14 [ DOI: doi:10.1016/j.cell.2018.05.017 Pubmed: 29887376 ]
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna (29-mer) (9 kDa, DNA from Escherichia coli)
- E.coli rfah-elongation complex (412 kDa, Complex from Escherichia coli)
- 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 alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Rna (5'-r(*gp*cp*ap*up*up*cp*ap*ap*ap*gp*cp*cp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli)
CryoEM structure of E.coli RNA polymerase elongation complex bound with NusG
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6c6u
Q-score: 0.442
Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA
Cell (2018) 173 pp. 1650-1662.e14 [ DOI: doi:10.1016/j.cell.2018.05.017 Pubmed: 29887376 ]
- Zinc ion (65 Da, Ligand)
- Dna (29-mer) (9 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Rna (5'-r(*gp*cp*ap*up*up*cp*ap*ap*ap*gp*cp*cp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase beta' (155 kDa, Protein from Escherichia coli (strain K12))
- E.coli nusg-elongation complex (414 kDa, Complex from Escherichia coli)
CryoEM structure of E.coli his pause elongation complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6asx
Q-score: 0.436
Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R
Mol Cell (2018) 69 pp. 802-815.e1 [ Pubmed: 29499135 DOI: doi:10.1016/j.molcel.2018.01.018 ]
- Rna (29-mer) (9 kDa, RNA from Salmonella enterica subsp. enterica serovar Typhimurium)
- Zinc ion (65 Da, Ligand)
- Dna (32-mer) (9 kDa, DNA from Salmonella enterica subsp. enterica serovar Typhimurium)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- E.coli his pause elongation complex (400 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Escherichia coli)
- Dna (32-mer) (9 kDa, DNA from Salmonella enterica subsp. enterica serovar Typhimurium)
CryoEM structure of E.coli his pause elongation complex without pause hairpin
Resolution: 5.5 Å
EM Method: Single-particle
Fitted PDBs: 6bjs
Q-score: 0.229
Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R
Mol Cell (2018) 69 pp. 802-815.e1 [ Pubmed: 29499135 DOI: doi:10.1016/j.molcel.2018.01.018 ]
- Rna (29-mer) (9 kDa, RNA from Salmonella enterica subsp. enterica serovar Typhimurium)
- Zinc ion (65 Da, Ligand)
- Dna (32-mer) (9 kDa, DNA from Salmonella enterica subsp. enterica serovar Typhimurium)
- 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 alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- E.coli his pause elongation complex without pause hairpin (400 kDa, Complex from Escherichia coli)
- Dna (32-mer) (9 kDa, DNA from Salmonella enterica subsp. enterica serovar Typhimurium)
Resolution: 7.6 Å
EM Method: Single-particle
Fitted PDBs: 5my1
Q-score: 0.113
Kohler R, Mooney RA, Mills DJ, Landick R, Cramer P
Science (2017) 356 pp. 194-197 [ Pubmed: 28408604 DOI: doi:10.1126/science.aal3059 ]
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli K-12)
- Transcribing rna polymerase (Complex from Escherichia coli K-12)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s7 (19 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s3 (25 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
- Translating ribosome (Complex from Escherichia coli K-12)
- 30s ribosomal protein s18 (8 kDa, Protein from Escherichia coli K-12)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
- In vitro reconstituted e. coli expressome consisting of transcribing rna polymerase and translating ribosome (Complex)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli K-12)