Mediator-PIC Early (Tail A + Upstream DNA Activator)
Resolution: 7.7 Å
EM Method: Single-particle
Fitted PDBs: 7uik
Q-score: 0.091
Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023) 83 pp. 574- [ DOI: doi:10.1016/j.molcel.2023.01.011 Pubmed: 36731470 ]
- Mediator of rna polymerase ii transcription subunit 5 (128 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Med-picearly (taila+activator & dna class 1) (Complex from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 2 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 14 (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 16 (111 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 15 (120 kDa, Protein from Saccharomyces cerevisiae S288C)
- Regulatory protein gal4 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 3 (43 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
Mediator-PIC Early (Composite Model)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7uio
Q-score: 0.239
Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023) 83 pp. 574- [ DOI: doi:10.1016/j.molcel.2023.01.011 Pubmed: 36731470 ]
- Mediator of rna polymerase ii transcription subunit 5 (128 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb1 (2 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Aspartic acid (133 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 3 (43 kDa, Protein from Saccharomyces cerevisiae S288C)
- Threonine (119 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb1 (162 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 16 (111 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 14 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription elongation factor s-ii (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 2 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Regulatory protein gal4 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae S288C)
- Alanine (89 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Med-picearly (Complex from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 15 (120 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
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 [ DOI: doi:10.1038/s41467-021-23684-x Pubmed: 34099686 ]
- Dna repair helicase rad25 (95 kDa, Protein from Baker's yeast)
- Dna repair helicase rad3 (89 kDa, Protein from Baker's yeast)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Baker's yeast)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Baker's yeast)
- Ternary complex of tfiih/rad4-rad23-rad33 with aaf damaged dna (420 MDa, Complex)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Baker's yeast)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Baker's yeast)
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 ]
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Baker's yeast)
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Baker's yeast)
- Damaged dna strand (8 kDa, DNA from synthetic construct)
- 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 Baker's yeast)
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 10 component complex of rad4-23, rad33 and tfiih on damaged dna (Complex)
- Dna repair helicase rad3 (89 kDa, Protein from Baker's yeast)
- 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))
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Baker's yeast)
Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 6xi8
Q-score: 0.185
van Eeuwen T, Li T, Kim HJ, Gorbea Colon JJ, Parker MI, Dunbrack RL, Garcia BA, Tsai KL, Murakami K
Sci Adv (2021) 7 [ Pubmed: 33827808 DOI: doi:10.1126/sciadv.abd4420 ]
- Aluminum fluoride (83 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Serine/threonine-protein kinase kin28 (34 kDa, Protein from Baker's yeast)
- Cyclin ccl1 (37 kDa, Protein from Baker's yeast)
- Ternary complex of kin28-ccl1-tfb3 from saccharomyces cerevisiae. (73 kDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 3 (7 kDa, Protein from Baker's yeast)
CryoEM structure of Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7kue
Q-score: 0.336
van Eeuwen T, Li T, Kim HJ, Gorbea Colon JJ, Parker MI, Dunbrack RL, Garcia BA, Tsai KL, Murakami K
Sci Adv (2021) 7 [ DOI: doi:10.1126/sciadv.abd4420 Pubmed: 33827808 ]
- Cyclin ccl1 (45 kDa, Protein from Baker's yeast)
- Ternary complex of kin28-ccl1-tfb3 from saccharomyces cerevisiae. (73 kDa, Complex from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Baker's yeast)
- Serine/threonine-protein kinase kin28 (35 kDa, Protein from Baker's yeast)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Aluminum fluoride (83 Da, Ligand)