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- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from pig)
- 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)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- 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 rpb3 (31 kDa, Protein from pig)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (217 kDa, Protein from pig)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iie (Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 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)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- General transcription factor iib (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from pig)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 4 (52 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- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
- General transcription factor iih (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from pig)
- 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)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
- Zinc ion (65 Da, Ligand)
- General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from pig)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iie (Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- 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)
- Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- General transcription factor iib (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from pig)
- General transcription factor iia (Complex from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
Initial DNA-lesion (Cy5) binding by XPC and TFIIH
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8ebs
Q-score: 0.274
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex (580 kDa, Complex 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 basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Dna (cy5) (16 kDa, DNA from synthetic construct)
- Dna (16 kDa, DNA from synthetic construct)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
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)