Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7o4i
Q-score: 0.4
Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P
Cell (2021) 184 pp. 4064-4072.e28 [ DOI: doi:10.1016/j.cell.2021.05.012 Pubmed: 34133942 ]
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Beryllium trifluoride ion (66 Da, Ligand)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Non-template dna, template dna (Complex from synthetic construct)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (95 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 initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Non-template dna (32 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Yeast rna polymerase ii transcription pre-initiation complex with initial transcription bubble (1 MDa, Complex)
- Transcription initiation factor, dna-directed rna polymerase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Baker's yeast)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb1 (73 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- General transcription and dna repair factor (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb3 (Complex 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))
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Baker's yeast)
- Template dna (32 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Baker's yeast)
- Tata-box-binding protein (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit (Complex 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))
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
map of the RNA polymerase lambda-based antitermination complex solved by cryo-EM
Resolution: 9.8 Å
EM Method: Single-particle
Fitted PDBs: 5ms0
Q-score: 0.069
Said N, Krupp F, Anedchenko E, Santos KF, Dybkov O, Huang YH, Lee CT, Loll B, Behrmann E, Burger J, Mielke T, Loerke J, Urlaub H, Spahn CMT, Weber G, Wahl MC
Nat Microbiol (2017) 2 pp. 17062-17062 [ Pubmed: 28452979 DOI: doi:10.1038/nmicrobiol.2017.62 ]
- Antitermination protein n (9 kDa, Protein from Escherichia phage lambda)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dnaii (11 kDa, DNA from Escherichia coli)
- Rna transcription bubble (4 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Lambdan-dependent antitermination complex (Complex from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Transcription termination/antitermination protein nusa (55 kDa, Protein from Escherichia coli K-12)
- Nascent rna (9 kDa, RNA from Escherichia coli)
- 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)
- Dnai (8 kDa, DNA from Escherichia coli)
- Transcription antitermination protein nusb (15 kDa, Protein from Escherichia coli K-12)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of yeast RNA polymerase III elongation complex at 3.9 A
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 5fj8
Q-score: 0.345
Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S, Kosinski J, Hagen WJ, Sachse C, Muller CW
Nature (2015) 528 pp. 231-236 [ Pubmed: 26605533 DOI: doi:10.1038/NATURE16143 ]
- Transcription bubble (290 kDa, Macromolecule from synthetic construct)
- Rna polymerase iii (690 kDa, Protein from Saccharomyces cerevisiae)
- S.cerevisiae rna polymerase iii elongation complex at 3.9 a (720 kDa, Sample)
Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5
Kassube SA, Jinek M, Fang J, Tsutakawa S, Nogales E
Nat Struct Mol Biol (2013) 20 pp. 892-899 [ Pubmed: 23748380 DOI: doi:10.1038/nsmb.2596 ]
- Recql5 (69 kDa, Protein from Homo sapiens)
- Human pol ii in complex with artificial transcription bubble and recql5 (615 kDa, Sample)
- Non-template strand (13 kDa, DNA from unidentified)
- Rna polymerase ii (517 kDa, Protein from Homo sapiens)
- Transcription bubble rna strand (6 kDa, RNA from unidentified)
- Template strand (8 kDa, DNA from unidentified)
Conformational flexibility of RNA polymerase III during transcriptional elongation
Fernandez-Tornero C, Bottcher B, Rashid UJ, Steuerwald U, Florchinger B, Devos DP, Lindner D, Muller CW
EMBO J (2010) 29 pp. 3762-3772 [ Pubmed: 20967027 DOI: doi:10.1038/emboj.2010.266 ]
- Transcription bubble (30 kDa, Macromolecule from synthetic construct)
- Rna polymerase iii (700 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase iii elongation complex (700 kDa, Sample)
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
Resolution: 19.8 Å
EM Method: Single-particle
Fitted PDBs: 3iyd
Q-score: 0.046
Hudson BP, Quispe J, Lara S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL
PNAS (2009) 106 pp. 19830-19835 [ DOI: doi:10.1073/pnas.0908782106 Pubmed: 19903881 ]
- Lac(icap)up-uv5-bubble (60 kDa, DNA from unidentified)
- Rna polymerase holoenzyme (sigma70) (460 kDa, Protein from Escherichia coli)
- Catabolite activator protein (50 kDa, Protein from Escherichia coli)
- E. coli rna polymerase holoenzyme (sigma70) and e. coli catabolite activator protein (cap) bound to 98-mer dna containing the lac promoter and engineered open transcription bubble (570 kDa, Sample)