Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8cen
Q-score: 0.269
Schilbach S, Wang H, Dienemann C, Cramer P
PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factors, and rna polymerase ii transcription factor b subunit 3 (Complex from Saccharomyces cerevisiae)
- Tata-binding protein (27 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 polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factors and mediator of rna polymerase ii transcription subunits (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunits (Complex from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 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 ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 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 helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with core mediator (2 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex from Synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 14 (84 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ceo
Q-score: 0.222
Schilbach S, Wang H, Dienemann C, Cramer P
PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with core mediator and the +1 nucleosome (2 MDa, Complex from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih (52 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 isoform 1 (72 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 14 (123 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Toa1 isoform 1 (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Mediator of rna polymerase ii transcription subunit 11 (13 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 rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- 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 rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome
Resolution: 15.0 Å
EM Method: Single-particle
Fitted PDBs: 6tda
Q-score: 0.081
Wagner FR, Dienemann C, Wang H, Stutzer A, Tegunov D, Urlaub H, Cramer P
Nature (2020) 579 pp. 448-451 [ DOI: doi:10.1038/s41586-020-2088-0 Pubmed: 32188943 ]
- Chromatin remodelling complex rsc ('remodels the structure of chromatin') bound to a nucleosome (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc8 (126 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Atpase domain of sth1 bound to the nucleosome (Complex from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Dna-i (72 kDa, DNA from synthetic construct)
- Rsc core (Complex from Saccharomyces cerevisiae S288C)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-j (73 kDa, DNA from synthetic construct)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
cryo-EM structure of transcription coactivator SAGA
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6t9i
Q-score: 0.38
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ Pubmed: 31969703 DOI: doi:10.1038/s41586-020-1933-5 ]
- Protein spt3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional activator spt7 (152 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 12 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga-associated factor 73 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unassigned sequence (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Saga complex (1 MDa, Complex from Saccharomyces cerevisiae S288C)
- Transcription initiation factor tfiid subunit 6 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 5 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional coactivator hfi1/ada1 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor spt20 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6t9j
Q-score: 0.458
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ Pubmed: 31969703 DOI: doi:10.1038/s41586-020-1933-5 ]
- Transcription initiation factor tfiid subunit 12 (61 kDa, Protein from Saccharomyces cerevisiae S288C)
- Saga tra1 module (450 kDa, Complex from Saccharomyces cerevisiae S288C)
- Transcription factor spt20 (67 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6t9k
Q-score: 0.473
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ DOI: doi:10.1038/s41586-020-1933-5 Pubmed: 31969703 ]
- Protein spt3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga-associated factor 73 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 5 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 12 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor spt20 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional coactivator hfi1/ada1 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unassigned sequence (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Saga core module (500 kDa, Complex from Saccharomyces cerevisiae S288C)
- Transcriptional activator spt7 (152 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 6 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
SAGA DUB module bound to a ubiqitinated nucleosome
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6t9l
Q-score: 0.394
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ Pubmed: 31969703 DOI: doi:10.1038/s41586-020-1933-5 ]
- Ubiquitin carboxyl-terminal hydrolase 8 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Widom601 dna (145-mer) (44 kDa, DNA from synthetic construct)
- Polyubiquitin-c (8 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Saga-associated factor 11 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Saga dub-ubiqitinated nucleosome complex (250 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Transcription and mrna export factor sus1 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga-associated factor 73 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga dub module (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin carboxyl-terminal hydrolase 8 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Widom601 dna (145-mer) (44 kDa, DNA from synthetic construct)
- Nucleosome (Complex from Xenopus laevis)
nucleosome-bound state of SAGA coactivator
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ Pubmed: 31969703 DOI: doi:10.1038/s41586-020-1933-5 ]
- Saga coactivator (450 kDa, Complex from Saccharomyces cerevisiae S288C)
Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6s01
Q-score: 0.529
Wang H, Farnung L, Dienemann C, Cramer P
Nat Struct Mol Biol (2020) 27 pp. 8-13 [ Pubmed: 31819277 DOI: doi:10.1038/s41594-019-0345-4 ]
- Histone proteins (Complex from Xenopus laevis)
- Wisdom 601 dna (165-mer) (51 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Wisdom 601 dna (165-mer) (Complex from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (Complex from Homo sapiens)
- Wisdom 601 dna (165-mer) (50 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H3k36me3 nucleosome-ledgf complex (250 kDa, Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)