Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7k01
Q-score: 0.331
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ Pubmed: 34099686 DOI: doi:10.1038/s41467-021-23684-x ]
- Dna repair helicase rad3 (89 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 tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Dna repair helicase rad25 (95 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))
- Zinc ion (65 Da, Ligand)
- Ternary complex of tfiih/rad4-rad23-rad33 with aaf damaged dna (420 MDa, Complex)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening
Resolution: 9.25 Å
EM Method: Single-particle
Fitted PDBs: 7k04
Q-score: 0.122
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ Pubmed: 34099686 DOI: doi:10.1038/s41467-021-23684-x ]
- Damaged dna strand (8 kDa, DNA from synthetic construct)
- Dna repair helicase rad3 (89 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 tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 10 component complex of rad4-23, rad33 and tfiih on damaged dna (Complex)
- Iron/sulfur cluster (351 Da, Ligand)
- Undamaged dna strand (8 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair protein rad4 (87 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair protein rad33 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Calcium ion (40 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 5oqj
Q-score: 0.249
Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P
Nature (2017) 551 pp. 204-209 [ Pubmed: 29088706 DOI: doi:10.1038/nature24282 ]
- Transcription factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 1 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Suppressor of stem-loop protein 1 (51 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))
- Transcription initiation factor iia subunit 2 (13 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))
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Polymerase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iie subunit alpha (57 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))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nontemplate dna (32 kDa, DNA from synthetic construct)
- Dna repair helicase rad25 (94 kDa, Protein 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 polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Tata-box-binding protein (27 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Initiation factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template dna (32 kDa, DNA from synthetic construct)
- Nucleic acid (Complex from synthetic construct)
- Rna polymerase ii transcription factor b subunit 2 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 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))
- Iron/sulfur cluster (351 Da, Ligand)
- 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 rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (3 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))
- Pre-initiation complex (pic) (1 MDa, Complex)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Mediator-RNA Polymerase II Pre-Initiation Complex Delta Mediator Tail (Focused Refinement)
Resolution: 15.3 Å
EM Method: Single-particle
Fitted PDBs: 5sva
Q-score: 0.049
Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD
Cell (2016) 166 pp. 1411-1422.e16 [ Pubmed: 27610567 DOI: doi:10.1016/j.cell.2016.08.050 ]
- Dna-directed rna polymerase ii subunit rpb2 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 1 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from yeast)
- Transcription initiation factor iia large subunit (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (Protein from yeast)
- Transcription initiation factor iif subunit beta (Protein from yeast)
- Suppressor of stem-loop protein 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 7 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 31 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 19 (Protein from yeast)
- Dna repair helicase rad25 (Protein from yeast)
- Tata-box-binding protein (Protein from Saccharomyces cerevisiae)
- Dna repair helicase rad3 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from yeast)
- Transcription factor tfiie subunit tfa1 (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb7 (Protein from yeast)
- Transcription initiation factor iif subunit gamma (Protein from yeast)
- Serine/threonine-protein kinase kin28 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 21 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 9 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 3 (Protein from yeast)
- Transcription initiation factor iib (Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 14 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 22 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 11 (Protein from yeast)
- Transcription factor tfiie subunit tfa2 (Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 18 (Protein from yeast)
- Mediator-rna polymerase ii pre-initiation complex delta mediator tail (1 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 8 (Protein from yeast)
- Cyclin ccl1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 6 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 10 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 4 (Protein from yeast)
- Transcription initiation factor iia subunit 2 (Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 4 (Protein from yeast)
- 108 bp his4 promoter fragment (DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 17 (Protein from yeast)
Mediator-RNA Polymerase II Pre-Initiation Complex
Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD
Cell (2016) 166 pp. 1411-1422.e16 [ Pubmed: 27610567 DOI: doi:10.1016/j.cell.2016.08.050 ]
- Transcription initiation factor iib (Protein from Saccharomyces cerevisiae)
- Suppressor of stem-loop protein 1 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (Protein from yeast)
- Transcription factor tfiie subunit tfa1 (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 10 (Protein from yeast)
- Transcription initiation factor iif subunit gamma (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 22 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 21 (Protein from yeast)
- Transcription initiation factor iif subunit beta (Protein from yeast)
- Tata-box-binding protein (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 11 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 3 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 5 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 20 (Protein from yeast)
- 108 bp his4 promoter fragment (DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 9 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 2 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 4 (Protein from yeast)
- Serine/threonine-protein kinase kin28 (Protein from yeast)
- Cyclin ccl1 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from yeast)
- Transcription initiation factor iia subunit 2 (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 17 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 31 (Protein from yeast)
- Transcription initiation factor iif subunit alpha (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from yeast)
- Transcription initiation factor iia large subunit (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 16 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 19 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 14 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 1 (Protein from yeast)
- Transcription factor tfiie subunit tfa2 (Protein from Saccharomyces cerevisiae)
- Dna repair helicase rad25 (Protein from yeast)
- Mediator-rna polymerase ii pre-initiation complex (2 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 6 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 8 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 7 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 2 (Protein from yeast)
- Dna repair helicase rad3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 15 (Protein from yeast)