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: 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 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)
RNA Polymerase I Closed Conformation 2 (CC2)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6rql
Q-score: 0.355
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW
Nat Commun (2019) 10 pp. 5543-5543 [ Pubmed: 31804486 DOI: doi:10.1038/s41467-019-13510-w ]
- Nontemplate strand (21 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn6 (102 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn3 (72 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn7 (60 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i closed complex conformation 2 (cc2) (Complex)
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Saccharomyces cerevisiae)
- Nucleic acid (Complex from synthetic construct)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor (Complex from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn11 (59 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i (Complex from Saccharomyces cerevisiae)
- Template strand (21 kDa, DNA from synthetic construct)
Structure of a yeast closed complex with distorted DNA (CCdist)
Resolution: 6.7 Å
EM Method: Single-particle
Fitted PDBs: 6gym
Q-score: 0.219
Dienemann C, Schwalb B, Schilbach S, Cramer P
Mol Cell (2019) 73 pp. 97-106.e4 [ Pubmed: 30472190 DOI: doi:10.1016/j.molcel.2018.10.014 ]
- Transcription initiation factor iie subunit alpha,transcription initiation factor iie subunit alpha,transcription initiation factor iie subunit alpha,transcription initiation factor iie subunit alpha,transcription initiation factor iie subunit alpha (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iia large subunit,transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb4,general transcription and dna repair factor iih subunit tfb4,rna polymerase ii transcription factor b subunit 4,general transcription and dna repair factor iih subunit tfb4,general transcription and dna repair factor iih subunit tfb4 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Complex (Complex)
- Polymerase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih helicase subunit xpd,general transcription and dna repair factor iih helicase subunit xpd,dna repair helicase rad3,dna repair helicase rad3,general transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit ssl1,general transcription and dna repair factor iih subunit ssl1,general transcription and dna repair factor iih subunit ssl1,general transcription and dna repair factor iih subunit ssl1,general transcription and dna repair factor iih subunit ssl1,general transcription and dna repair factor iih subunit ssl1,general transcription and dna repair factor iih subunit ssl1 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb1,general transcription and dna repair factor iih subunit tfb1,rna polymerase ii transcription factor b subunit 1,general transcription and dna repair factor iih subunit tfb1,rna polymerase ii transcription factor b subunit 1,general transcription and dna repair factor iih subunit tfb1,general transcription and dna repair factor iih subunit tfb1,general transcription and dna repair factor iih subunit tfb1,rna polymerase ii transcription factor b subunit 1,general transcription and dna repair factor iih subunit tfb1,rna polymerase ii transcription factor b subunit 1,general transcription and dna repair factor iih subunit tfb1,general transcription and dna repair factor iih subunit tfb1 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nucleic acid (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb2,general transcription and dna repair factor iih subunit tfb2,general transcription and dna repair factor iih subunit tfb2,general transcription and dna repair factor iih subunit tfb2,general transcription and dna repair factor iih subunit tfb2,general transcription and dna repair factor iih subunit tfb2,general transcription and dna repair factor iih subunit tfb2 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Unknown protein (3 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template dna (his4) (23 kDa, DNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Non-template dna (his4) (23 kDa, DNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih helicase subunit xpb,general transcription and dna repair factor iih helicase subunit xpb,dna repair helicase rad25,general transcription and dna repair factor iih helicase subunit xpb,dna repair helicase rad25,general transcription and dna repair factor iih helicase subunit xpb,general transcription and dna repair factor iih helicase subunit xpb,dna repair helicase rad25,general transcription and dna repair factor iih helicase subunit xpb,dna repair helicase rad25,general transcription and dna repair factor iih helicase subunit xpb,general transcription and dna repair factor iih helicase subunit xpb,dna repair helicase rad25,general transcription and dna repair factor iih helicase subunit xpb,dna repair helicase rad25,general transcription and dna repair factor iih helicase subunit xpb,general transcription and dna repair factor iih helicase subunit xpb (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))