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)
TFIIH in a post-translocated state (with ADP-BeF3)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7nvx
Q-score: 0.305
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Tfiih (with adp-bef3) (490 kDa, Complex)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
Resolution: 7.3 Å
EM Method: Single-particle
Fitted PDBs: 7nvy
Q-score: 0.118
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)
- Rpb1 (217 kDa, Protein from Pig)
- 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)
- 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)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with closed promoter dna in proximal position (1 MDa, Complex)
- 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)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 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)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with closed promoter DNA in distal position
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 7nvz
Q-score: 0.111
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)
- Rpb1 (217 kDa, Protein from Pig)
- Rna polymerase ii pre-initiation complex with closed promoter dna in distal position (1 MDa, Complex)
- 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)
- 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)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- 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)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 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)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with open promoter DNA
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 7nw0
Q-score: 0.119
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Rna polymerase ii pre-initiation complex with open promoter dna (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- 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 iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)