Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7zsa
Q-score: 0.342
Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 226-232 [ Pubmed: 36411341 DOI: doi:10.1038/s41594-022-00865-w ]
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Non-template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with the +1 nucleosome and ntp (1 MDa, Complex from Saccharomyces cerevisiae)
- Tata-box-binding protein (28 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 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 rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb1 (73 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Human Mediator with RNA Polymerase II Pre-initiation complex
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7nvr
Q-score: 0.171
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Pol complex and mediator of rna polymerase ii transcription (Complex from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Transcription initiation factors (Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Human mediator with rna polymerase ii pre-initiation complex (Complex)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Template (32 kDa, DNA from Human mastadenovirus C)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Nt and template (Complex from Human mastadenovirus C)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Unassigned peptide (med14) (1 kDa, Protein from Homo sapiens)
- Unassigned peptide (med17) (954 Da, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Nt (32 kDa, DNA from Human mastadenovirus C)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Unassigned peptide (med6) (1 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Unassigned peptides (med29 or med30) (Complex from Trichoplusia ni)
TFIIH in a pre-translocated state (without ADP-BeF3)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7nvw
Q-score: 0.279
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Tfiih (without adp-bef3) (490 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)