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 ]
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Transcription complex paused at ops site, assembled on a not fully complementary scaffold (399 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein 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 ]
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Transcription complex paused at ops with fully recruited rfah (417 kDa, Complex)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein 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 ]
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (12 kDa, DNA 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)
- 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 beta' (156 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein 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 ]
- Transcription antitermination protein rfah and dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Rna and dna (Complex 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 omega (10 kDa, Protein from Escherichia coli)
- Rna (5 kDa, RNA 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, assembled on not completely complementary scaffold, bound to rfah (417 kDa, Complex)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8cen
Q-score: 0.269
Schilbach S, Wang H, Dienemann C, Cramer P
PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factors, and rna polymerase ii transcription factor b subunit 3 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 14 (84 kDa, Protein from Saccharomyces cerevisiae)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunits (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with core mediator (2 MDa, Complex)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factors and mediator of rna polymerase ii transcription subunits (Complex from Saccharomyces cerevisiae)
- Dna (Complex from Synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7qxi
Q-score: 0.364
Ye F, Gao F, Liu X, Buck M, Zhang X
Sci Adv (2022) 8 pp. eadd3479-eadd3479 [ Pubmed: 36542713 DOI: doi:10.1126/sciadv.add3479 ]
- Template dna promoter (19 kDa, DNA from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Non-template promoter dna (Complex from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma-54 factor (56 kDa, Protein from Klebsiella pneumoniae)
- Non-template promoter dna (19 kDa, DNA from Klebsiella pneumoniae)
- Template dna promoter (Complex from Klebsiella pneumoniae)
- Cryo-em structure of rna polymerase-sigma54 holo enzyme with promoter dna closed complex (500 kDa, Complex)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunits alpha, beta, beta' and omega (Complex from Escherichia coli K-12)
- Rna polymerase sigma-54 factor (Complex from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of SoxS-dependent transcription activation complex with micF promoter DNA
Resolution: 4.55 Å
EM Method: Single-particle
Fitted PDBs: 7w5w
Q-score: 0.332
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)
- Dna (Complex)
- Magnesium ion (24 Da, Ligand)
- Soxs-dependent transcription activation complex with micf 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)
- Micf promoter dna reverse strand (21 kDa, DNA from Escherichia coli)
- Micf promoter dna forward strand (21 kDa, DNA from Escherichia coli)
- 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)
Cryo-EM structure of SoxS-dependent transcription activation complex with zwf promoter DNA
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7w5x
Q-score: 0.47
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)
- Dna (Complex)
- Zwf promoter dna reverse strand (23 kDa, DNA from Escherichia coli)
- Soxs-dependent transcription activation complex with zwf 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)
- Zwf promoter dna forward strand (23 kDa, DNA from Escherichia coli)
- 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)
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)
Structure of Vaccinia Virus DNA-dependent RNA polymerase elongation complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6rid
Q-score: 0.579
Hillen HS, Bartuli J, Grimm C, Dienemann C, Bedenk K, Szalay AA, Fischer U, Cramer P
Cell (2019) 179 pp. 1525- [ DOI: doi:10.1016/j.cell.2019.11.023 Pubmed: 31835031 ]
- Dna-dependent rna polymerase subunit rpo132 (Complex from Vaccinia virus GLV-1h68)
- Dna-directed rna polymerase 35 kda subunit (35 kDa, Protein from Vaccinia virus GLV-1h68)
- Zinc ion (65 Da, Ligand)
- Dna-dependent rna polymerase subunit rpo132 (133 kDa, Protein from Vaccinia virus GLV-1h68)
- Vaccinia virus dna-dependent rna polymerase elongation complex (450 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Dna-dependent rna polymerase subunit rpo147 (146 kDa, Protein from Vaccinia virus GLV-1h68)
- Nucleic acids (Complex from Vaccinia virus GLV-1h68)
- Dna-dependent rna polymerase subunit rpo18 (17 kDa, Protein from Vaccinia virus GLV-1h68)
- Template strand dna (14 kDa, DNA from Vaccinia virus)
- Dna-directed rna polymerase subunit (21 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-directed rna polymerase 30 kda polypeptide (29 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-dependent rna polymerase subunit rpo7 (7 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-directed rna polymerase subunits (Complex from Vaccinia virus GLV-1h68)
- Dna-directed rna polymerase 19 kda subunit (19 kDa, Protein from Vaccinia virus GLV-1h68)
- Non-template strand dna (14 kDa, DNA from Vaccinia virus)
- Rna (9 kDa, RNA from Vaccinia virus)