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 ]
- Transcription elongation complex paused at ops site, assembled on fully complementary nucleic acid scaffold (399 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Rna (5'-r(p*up*gp*gp*cp*gp*gp*up*ap*gp*cp*gp*u)-3') (5 kDa, RNA from Escherichia coli)
- Dna and rna (Complex 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)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Non-template dna (35-mer) (12 kDa, DNA from Escherichia coli)
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 ]
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA 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)
- Magnesium ion (24 Da, Ligand)
- Transcription complex paused at ops site with fully recruited rfah (417 kDa, Complex)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
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 ]
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA 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)
- Transcription complex paused at ops site, assembled on not fully complementary nucleic acid scaffold, bound to disulfide-bridged (autoinhibited) rfah (417 kDa, Complex)
- Rna (5 kDa, RNA 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 ]
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Template dna (12 kDa, DNA 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)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Transcription complex paused at ops site, bound to fully activated rfah, assembled on not fully complementary nucleic acid scaffold (417 kDa, Complex)
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 ]
- Zinc ion (65 Da, Ligand)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Transcription complex paused at ops site, assembled on a not fully complementary scaffold (399 kDa, Complex)
- 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)
- Rna (5 kDa, RNA 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 ]
- Zinc ion (65 Da, Ligand)
- Template dna (12 kDa, DNA from Escherichia coli)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA 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 (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops with fully recruited rfah (417 kDa, Complex)
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 ]
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops site with autoinhibited, disulfide-bridged rfah (417 kDa, Complex)
- 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)
- Rna (5 kDa, RNA 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 ]
- Transcription elongation complex (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna and rna (Complex from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription elongation complex paused at ops site with bound rfah after nucleotide addition, assembled on fully complementary scaffold (417 kDa, Complex)
- 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)
- Transcription antitermination protein rfah (18 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)
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 ]
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Transcription complex paused at ops site, assembled on a fully complementary nucleic acid scaffold, bound to rfah and nusa (472 kDa, Complex)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription termination/antitermination protein nusa (55 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)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA 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 ]
- Zinc ion (65 Da, Ligand)
- Transcription complex paused at ops site, assembled on not completely complementary scaffold, bound to rfah (417 kDa, Complex)
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Template dna (12 kDa, DNA 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)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)