Structure of Pol II-TC-NER-STK19 complex, consensus map
Ramadhin AR, Lee SH, Zhou D, Salmazo A, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA
Mol Cell (2024) 84 pp. 4740-4757.e12 [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Dna-directed rna polymerase ii subunit e (Protein from Sus scrofa domesticus)
- Non-template strand dna (DNA from Homo sapiens)
- Inactive serine/threonine-protein kinase 19 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa domesticus)
- E3 ubiquitin-protein ligase rbx1 (Protein from Homo sapiens)
- Nedd8 (Protein from Homo sapiens)
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Cullin-4a (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from Sus scrofa domesticus)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa domesticus)
- Template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa domesticus)
- Rna (RNA from Homo sapiens)
- Dna excision repair protein ercc-6 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit rpb7 (Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa domesticus)
- Ternary complex of pol ii-tc-ner-stk19, consensus map (1 MDa, Complex from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (Protein from Homo sapiens)
Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8rap
Q-score: 0.24
Rengachari S, Hainthaler T, Oberthuer C, Lidschreiber M, Cramer P
Nat Struct Mol Biol (2025) 32 pp. 339-345 [ Pubmed: 39424994 DOI: doi:10.1038/s41594-024-01409-0 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (18 kDa, DNA from Human immunodeficiency virus 2)
- Dna (Complex from Human immunodeficiency virus 2)
- Helicase sen1 (252 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand (17 kDa, DNA from Human immunodeficiency virus 2)
- Zinc ion (65 Da, Ligand)
- Rna (Complex from Human immunodeficiency virus 2)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factors (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Rna (11 kDa, RNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Beryllium trifluoride ion (66 Da, Ligand)
- Transcription elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Tertiary complex of rna polymerase ii with elongation factors elf1, spt4, spt5 and the termination factor sen1 (Complex)
- Transcription elongation factor 1 (16 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of backtracked Pol II in complex with Rad26
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8tvs
Q-score: 0.305
Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE
PNAS (2024) 121 pp. e2314245121-e2314245121 [ Pubmed: 38194460 DOI: doi:10.1073/pnas.2314245121 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 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)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna repair and recombination protein rad26 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna (nts) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of backtracked rna polymerase ii elongation complex with rad26 (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (35 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)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna (ts) (14 kDa, DNA from synthetic construct)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7uif
Q-score: 0.127
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 ]
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator-pic early (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 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 22 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 8 (25 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 19 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription elongation factor s-ii (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 9 (17 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)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iif subunit beta (46 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 20 (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae S288C)
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 [ DOI: doi:10.1038/s41594-022-00865-w Pubmed: 36411341 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 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 polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 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)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- General transcription and dna repair factor iih subunit tfb1 (73 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Non-template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Tata-box-binding protein (28 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 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 rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Yeast rna polymerase ii transcription pre-initiation complex with the +1 nucleosome and ntp (1 MDa, Complex from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
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)
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)
Structure of the p53/RNA polymerase II assembly
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 6xre
Q-score: 0.134
Liou SH, Singh SK, Singer RH, Coleman RA, Liu WL
Commun Biol (2021) 4 pp. 397-397 [ DOI: doi:10.1038/s42003-021-01934-4 Pubmed: 33767390 ]
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Cellular tumor antigen p53 (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- P53/rna polymerase ii assembly (Complex)
- Cellular tumor antigen p53 (Complex from Homo sapien)
Structure of the human Mediator-bound transcription pre-initiation complex
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7lbm
Q-score: 0.074
Abdella R, Talyzina A, Chen S, Inouye CJ, Tjian R, He Y
Science (2021) 372 pp. 52-56 [ DOI: doi:10.1126/science.abg3074 Pubmed: 33707221 ]
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Promoter dna (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 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)
- General transcription factors (300 kDa, Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Mediator-bound pre-initiation complex (2 MDa, Complex)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- 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)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- 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)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 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 rpabc4 (7 kDa, Protein from Homo sapiens)
- Tfiih (500 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 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)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Cyclin-h and associated factors (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- 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)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Rna polymerase ii (520 kDa, Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Super core promoter sense strand (31 kDa, DNA from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- 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 (1 MDa, Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Super core promoter antisense strand (30 kDa, DNA from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 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)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
Structure of a yeast closed complex with distorted DNA (core CCdist)
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6gyl
Q-score: -0.004
Dienemann C, Schwalb B, Schilbach S, Cramer P
Mol Cell (2019) 73 pp. 97-106.e4 [ Pubmed: 30472190 DOI: doi:10.1016/j.molcel.2018.10.014 ]
- Tifs (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Baker's yeast)
- Gat1 promoter dna (17 kDa, DNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Baker's yeast)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Baker's yeast)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Gat1 promoter dna (17 kDa, DNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iie subunit alpha,tfa1,tfa1 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Baker's yeast)
- Pre-initiation complex (Complex)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Polymerase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Baker's yeast)
- Transcription initiation factor iia large subunit,transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Baker's yeast)
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Baker's yeast)
- Nucleic acids (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Baker's yeast)