RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription factor iie (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- General transcription factor iib (Complex from Homo sapiens)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8byq
Q-score: 0.187
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iih (Complex from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription factor iie (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iib (Complex from Homo sapiens)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex (PIC1)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ml0
Q-score: 0.417
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ Pubmed: 35051353 DOI: doi:10.1016/j.molcel.2021.12.020 ]
- Dna-directed rna polymerase subunit (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (20 kDa, DNA from Saccharomyces cerevisiae)
- Rna polymerase ii pre-initiation complex (pic1) (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna+tbp+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Template strand dna (20 kDa, DNA from Saccharomyces cerevisiae)
- Tfiih (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
RNA polymerase II pre-initiation complex (PIC2)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7ml1
Q-score: 0.291
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ Pubmed: 35051353 DOI: doi:10.1016/j.molcel.2021.12.020 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna+tfiia+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 (58 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Tfiih (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii pre-initiation complex (pic2) (Complex from Saccharomyces cerevisiae)
RNA polymerase II pre-initiation complex (PIC3)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ml2
Q-score: 0.241
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ Pubmed: 35051353 DOI: doi:10.1016/j.molcel.2021.12.020 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna+tbp+tfiia+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 (58 kDa, Protein from Saccharomyces cerevisiae)
- Template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0004860.mrna.1.cds.1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Tfiih (Complex from Saccharomyces cerevisiae)
- Rna polymerase ii pre-initiation complex (pic3) (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih (52 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
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 [ DOI: doi:10.1038/s41586-021-03554-8 Pubmed: 33902107 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Pol complex and mediator of rna polymerase ii transcription (Complex from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Nt and template (Complex from Human mastadenovirus C)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Unassigned peptide (med6) (1 kDa, Protein from Homo sapiens)
- Human mediator with rna polymerase ii pre-initiation complex (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Unassigned peptide (med17) (954 Da, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Unassigned peptide (med14) (1 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- Template (32 kDa, DNA from Human mastadenovirus C)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Nt (32 kDa, DNA from Human mastadenovirus C)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Transcription initiation factors (Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Unassigned peptides (med29 or med30) (Complex from Trichoplusia ni)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 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)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-021-03554-8 Pubmed: 33902107 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii pre-initiation complex with closed promoter dna in proximal position (1 MDa, Complex)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, 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 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
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 [ DOI: doi:10.1038/s41586-021-03554-8 Pubmed: 33902107 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, 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 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with closed promoter dna in distal position (1 MDa, Complex)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
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 [ DOI: doi:10.1038/s41586-021-03554-8 Pubmed: 33902107 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with open promoter dna (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, 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 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
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 [ DOI: doi:10.1016/j.cell.2016.08.050 Pubmed: 27610567 ]
- Tata-box-binding protein (Protein from Saccharomyces cerevisiae)
- 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)
- Rna polymerase ii transcription factor b subunit 3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 10 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 11 (Protein from yeast)
- Dna repair helicase rad25 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 18 (Protein from yeast)
- Transcription initiation factor iif subunit gamma (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from yeast)
- Transcription initiation factor iif subunit alpha (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (Protein from yeast)
- Transcription initiation factor iib (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (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)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from yeast)
- Dna repair helicase rad3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 22 (Protein from yeast)
- Transcription initiation factor iif subunit beta (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from yeast)
- Transcription factor tfiie subunit tfa1 (Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 5 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 21 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 19 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb7 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 8 (Protein from yeast)
- Mediator-rna polymerase ii pre-initiation complex delta mediator tail (1 MDa, Complex)
- Serine/threonine-protein kinase kin28 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from yeast)
- Suppressor of stem-loop protein 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 14 (Protein from yeast)
- Transcription factor tfiie subunit tfa2 (Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 7 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 6 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 31 (Protein from yeast)
- Cyclin ccl1 (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)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from yeast)
- Transcription initiation factor iia subunit 2 (Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (Protein from yeast)