STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR
Resolution: 5.8 Å
EM Method: Single-particle
Fitted PDBs: 5oqm
Q-score: 0.183
Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P
Nature (2017) 551 pp. 204-209 [ DOI: doi:10.1038/nature24282 Pubmed: 29088706 ]
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 6 (32 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))
- Mediator of rna polymerase ii transcription subunit 10 (17 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))
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription (Complex from Saccharomyces cerevisiae)
- Transcription factor tfiie subunit (59 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase (Complex from Saccharomyces cerevisiae)
- Pre-initiation complex with core mediator (pic-cmed) (1 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iif subunit beta (46 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 11 (13 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))
- Mediator of rna polymerase ii transcription subunit 19 (24 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))
- 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 rpb9 (14 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))
- General transcription and dna repair factor iih subunit ssl1 (51 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))
- Transcription initiation factor iif subunit alpha (83 kDa, Protein from Saccharomyces cerevisiae)
- Unknown protein (3 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 4 (33 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- General transcription and dna repair factor iih subunit tfb4 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template dna (32 kDa, DNA from synthetic construct)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 14 (84 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))
- Transcription initiation factor iie subunit beta (37 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))
- General transcription and dna repair factor iih subunit tfb2 (60 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 8 (25 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))
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii transcription factor b (Complex from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (94 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))
- Nontemplate dna (32 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih subunit tfb1 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Mediator of rna polymerase ii transcription subunit 31,mediator of rna polymerase ii transcription subunit 31 (16 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))
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 [ DOI: doi:10.1038/nature24282 Pubmed: 29088706 ]
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 2 (48 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 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))
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Initiation factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iif subunit beta (46 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))
- Dna-directed rna polymerase ii subunit rpb11 (13 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))
- Polymerase (Complex 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))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad3 (89 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 polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nucleic acid (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (138 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 1 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template dna (32 kDa, DNA from synthetic construct)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-initiation complex (pic) (1 MDa, Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 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))
- Rna polymerase ii transcription factor b subunit 5 (8 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))
- Transcription initiation factor iie subunit alpha (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Suppressor of stem-loop protein 1 (51 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))
- Nontemplate dna (32 kDa, DNA from synthetic construct)
- Dna repair helicase rad25 (94 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 rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Architecture of the RNA polymerase II-Mediator core transcription initiation complex
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 4v1m
Q-score: 0.151
Plaschka C, Lariviere L, Wenzeck L, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P
Nature (2015) 518 pp. 376-380 [ DOI: doi:10.1038/nature14229 Pubmed: 25652824 ]
- Template dna (DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (DNA from synthetic construct)
- Rna (RNA from synthetic construct)
- Pol ii-dna/rna (570 kDa, Sample)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 3 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (192 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (18 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (139 kDa, Protein from Saccharomyces cerevisiae)
Architecture of the RNA polymerase II-Mediator core transcription initiation complex
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 4v1n
Q-score: 0.129
Plaschka C, Lariviere L, Wenzeck L, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P
Nature (2015) 518 pp. 376-380 [ DOI: doi:10.1038/nature14229 Pubmed: 25652824 ]
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (18 kDa, Protein from Saccharomyces cerevisiae)
- Rna (RNA from synthetic construct)
- Transcription initiation factor iif subunit beta (47 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces mikatae)
- Template dna (DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 3 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (139 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (20 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (192 kDa, Protein from Saccharomyces cerevisiae)
- Citc (750 kDa, Sample)
Architecture of the RNA polymerase II-Mediator core transcription initiation complex
Resolution: 9.7 Å
EM Method: Single-particle
Fitted PDBs: 4v1o
Q-score: 0.116
Plaschka C, Lariviere L, Wenzeck L, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P
Nature (2015) 518 pp. 376-380 [ DOI: doi:10.1038/nature14229 Pubmed: 25652824 ]
- Mediator of rna polymerase ii transcription subunit 14 (85 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (18 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (79 kDa, Protein from Saccharomyces cerevisiae)
- Rna (RNA from synthetic construct)
- Transcription initiation factor iif subunit beta (47 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces mikatae)
- Template dna (DNA from synthetic construct)
- Mediator of rna polymerase ii transcription subunit 19 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 3 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 10 (18 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (33 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Citc-cmed (1 MDa, Sample)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 7 (26 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 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (139 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (20 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (192 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)