E. coli RNA polymerase paused at ops site
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8pdy
Q-score: 0.409
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*up*gp*gp*cp*gp*gp*up*ap*gp*cp*gp*u)-3') (5 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Non-template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Transcription elongation complex paused at ops site, assembled on fully complementary nucleic acid scaffold (399 kDa, Complex)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8pen
Q-score: 0.451
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Template dna (12 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)
- Rna (5 kDa, RNA from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription complex paused at ops site with fully recruited rfah (417 kDa, Complex)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8pfg
Q-score: 0.471
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops site, assembled on not fully complementary nucleic acid scaffold, bound to disulfide-bridged (autoinhibited) rfah (417 kDa, Complex)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Non-template dna (12 kDa, DNA from Escherichia coli)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8pfj
Q-score: 0.434
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription complex paused at ops site, bound to fully activated rfah, assembled on not fully complementary nucleic acid scaffold (417 kDa, Complex)
- Non-template dna (12 kDa, DNA from Escherichia coli)
E. coli RNA polymerase paused at ops site (non-complementary scaffold)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8ph9
Q-score: 0.512
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops site, assembled on a not fully complementary scaffold (399 kDa, Complex)
- Rna (5 kDa, RNA from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
E. coli transcription complex paused at ops site with fully recruited RfaH
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8phk
Q-score: 0.436
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops with fully recruited rfah (417 kDa, Complex)
- Rna (5 kDa, RNA from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8pib
Q-score: 0.494
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops site with autoinhibited, disulfide-bridged rfah (417 kDa, Complex)
- Rna and dna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
backtracked E. coli transcription complex paused at ops site and bound to RfaH
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8pid
Q-score: 0.469
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Template dna (12 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)
- Rna (5'-r(p*up*gp*gp*cp*gp*gp*up*ap*gp*cp*gp*up*gp*c)-3') (6 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Transcription elongation complex (Complex from Escherichia coli)
- Transcription elongation complex paused at ops site with bound rfah after nucleotide addition, assembled on fully complementary scaffold (417 kDa, Complex)
- Non-template dna (12 kDa, DNA from Escherichia coli)
E. coli transcription complex paused at ops site and bound to RfaH and NusA
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8pil
Q-score: 0.421
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Template dna (12 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)
- Rna (5 kDa, RNA from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Transcription termination/antitermination protein nusa (55 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription complex paused at ops site, assembled on a fully complementary nucleic acid scaffold, bound to rfah and nusa (472 kDa, Complex)
- Non-template dna (12 kDa, DNA from Escherichia coli)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8pim
Q-score: 0.395
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Transcription complex paused at ops site, assembled on not completely complementary scaffold, bound to rfah (417 kDa, Complex)
- Non-template dna (12 kDa, DNA from Escherichia coli)