RNA Polymerase II dimer (Class 1)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7ozn
Q-score: 0.387
Aibara S, Dienemann C, Cramer P
Nucleic Acids Res (2021) 49 pp. 10747-10755 [ Pubmed: 34530439 DOI: doi:10.1093/nar/gkab783 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Rpb1 (217 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Rpb10 (7 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii dimer (1 MDa, Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
Structure of activated transcription complex Pol II-DSIF-PAF-SPT6 (Map A)
Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P
Nature (2018) 560 pp. 607-612 [ DOI: doi:10.1038/s41586-018-0440-4 Pubmed: 30135578 ]
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Nucleic acids (Complex from synthetic construct)
- Associated proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Ctr9,rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein ctr9 homolog (125 kDa, Protein from Homo sapiens)
- Leo1,leo1,rna polymerase-associated protein leo1 (84 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit g (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Transcription elongation factor spt6,transcription elongation factor spt6,transcription elongation factor spt6 (198 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit c (31 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii (Complex from Sus scrofa)
- Paf1,rna polymerase ii-associated factor 1 homolog,rna polymerase ii-associated factor 1 homolog (67 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii-dsif-paf-spt6 elongation complex (ec*) (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Cdc73 (1 kDa, Protein from Homo sapiens)
Architecture of the RNA polymerase II-Mediator core transcription initiation complex
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 4v1m
Q-score: 0.151
Plaschka C, Lariviere L, Wenzeck L, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P
Nature (2015) 518 pp. 376-380 [ DOI: doi:10.1038/nature14229 Pubmed: 25652824 ]
- Template dna (DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (DNA from synthetic construct)
- Rna (RNA from synthetic construct)
- Pol ii-dna/rna (570 kDa, Sample)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 3 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (192 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (18 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (139 kDa, Protein from Saccharomyces cerevisiae)
Architecture of the RNA polymerase II-Mediator core transcription initiation complex
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 4v1n
Q-score: 0.129
Plaschka C, Lariviere L, Wenzeck L, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P
Nature (2015) 518 pp. 376-380 [ DOI: doi:10.1038/nature14229 Pubmed: 25652824 ]
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (18 kDa, Protein from Saccharomyces cerevisiae)
- Rna (RNA from synthetic construct)
- Transcription initiation factor iif subunit beta (47 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces mikatae)
- Template dna (DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 3 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (139 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (20 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (192 kDa, Protein from Saccharomyces cerevisiae)
- Citc (750 kDa, Sample)
Architecture of the RNA polymerase II-Mediator core transcription initiation complex
Resolution: 9.7 Å
EM Method: Single-particle
Fitted PDBs: 4v1o
Q-score: 0.116
Plaschka C, Lariviere L, Wenzeck L, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P
Nature (2015) 518 pp. 376-380 [ DOI: doi:10.1038/nature14229 Pubmed: 25652824 ]
- Mediator of rna polymerase ii transcription subunit 14 (85 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (18 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (79 kDa, Protein from Saccharomyces cerevisiae)
- Rna (RNA from synthetic construct)
- Transcription initiation factor iif subunit beta (47 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces mikatae)
- Template dna (DNA from synthetic construct)
- Mediator of rna polymerase ii transcription subunit 19 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 3 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 10 (18 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (33 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Citc-cmed (1 MDa, Sample)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 7 (26 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 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (139 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 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 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (20 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (192 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)