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 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 31 (Protein from yeast)
- Transcription initiation factor iif subunit beta (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from yeast)
- Dna repair helicase rad3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 4 (Protein from yeast)
- Cyclin ccl1 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from yeast)
- 108 bp his4 promoter fragment (DNA from Saccharomyces cerevisiae)
- Transcription initiation factor iib (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 7 (Protein from yeast)
- Dna repair helicase rad25 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 17 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 22 (Protein from yeast)
- Transcription initiation factor iif subunit alpha (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 19 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 4 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb7 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 9 (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)
- Mediator of rna polymerase ii transcription subunit 21 (Protein from yeast)
- Serine/threonine-protein kinase kin28 (Protein from yeast)
- Tata-box-binding protein (Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (Protein from yeast)
- Transcription factor tfiie subunit tfa1 (Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 20 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 10 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 6 (Protein from yeast)
- Transcription initiation factor iia large subunit (Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 5 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (Protein from yeast)
- Suppressor of stem-loop protein 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 14 (Protein from yeast)
- Transcription initiation factor iif subunit gamma (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 11 (Protein from yeast)
- Transcription factor tfiie subunit tfa2 (Protein from Saccharomyces cerevisiae)
Mediator-RNA Polymerase II Pre-Initiation Complex Delta TFIIE-IIH (Focused refinement)
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 ]
- Mediator of rna polymerase ii transcription subunit 31 (Protein from yeast)
- Transcription initiation factor iif subunit beta (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb7 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 4 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (Protein from yeast)
- 108 bp his4 promoter fragment (DNA from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 16 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 18 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 7 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 3 (Protein from yeast)
- Mediator-rna polymerase ii pre-initiation complex delta tfiie-iih (focused refinement) (1 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 17 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 22 (Protein from yeast)
- Transcription initiation factor iif subunit alpha (Protein from yeast)
- Transcription initiation factor iib (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 9 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 8 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 21 (Protein from yeast)
- Tata-box-binding protein (Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from yeast)
- Transcription initiation factor iia subunit 2 (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 20 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 10 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 15 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 6 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 2 (Protein from yeast)
- Transcription initiation factor iia large subunit (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 14 (Protein from yeast)
- Transcription initiation factor iif subunit gamma (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 11 (Protein from yeast)
Mediator-RNA Polymerase II Pre-Initiation Complex
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 ]
- Mediator of rna polymerase ii transcription subunit 31 (Protein from yeast)
- Transcription initiation factor iif subunit beta (Protein from yeast)
- Mediator-rna polymerase ii pre-initiation complex (2 MDa, Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb7 (Protein from yeast)
- Dna repair helicase rad3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 4 (Protein from yeast)
- Cyclin ccl1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 2 (Protein from yeast)
- 108 bp his4 promoter fragment (DNA from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 16 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 18 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 7 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 3 (Protein from yeast)
- Dna repair helicase rad25 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 17 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 22 (Protein from yeast)
- Transcription initiation factor iif subunit alpha (Protein from yeast)
- Transcription initiation factor iib (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 4 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 9 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 8 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 21 (Protein from yeast)
- Serine/threonine-protein kinase kin28 (Protein from yeast)
- Tata-box-binding protein (Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from yeast)
- Transcription initiation factor iia subunit 2 (Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (Protein from yeast)
- Transcription factor tfiie subunit tfa1 (Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 20 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 4 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc 1 (Protein from yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from yeast)
- Rna polymerase ii transcription factor b subunit 1 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 10 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 15 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 6 (Protein from yeast)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 2 (Protein from yeast)
- Transcription initiation factor iia large subunit (Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 5 (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 14 (Protein from yeast)
- Suppressor of stem-loop protein 1 (Protein from yeast)
- Transcription initiation factor iif subunit gamma (Protein from yeast)
- Mediator of rna polymerase ii transcription subunit 11 (Protein from yeast)
- Transcription factor tfiie subunit tfa2 (Protein from Saccharomyces cerevisiae)
Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, Nogales E
Cell (2013) 152 pp. 120-131 [ Pubmed: 23332750 DOI: doi:10.1016/j.cell.2012.12.005 ]
- Transcription factor scp (1 MDa, Protein from Homo sapiens)
- Transcription factor ii-a (1 MDa, Protein from Homo sapiens)
- Tfiid-tfiia-scp (rearranged) (1 MDa, Sample)
- Transcription factor ii-d (1 MDa, Protein from Homo sapiens)
Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5
Kassube SA, Jinek M, Fang J, Tsutakawa S, Nogales E
Nat Struct Mol Biol (2013) 20 pp. 892-899 [ DOI: doi:10.1038/nsmb.2596 Pubmed: 23748380 ]
- Rna polymerase ii (517 kDa, Protein from Homo sapiens)
- Human pol ii in complex with artificial transcription bubble and recql5 (615 kDa, Sample)
- Non-template strand (13 kDa, DNA from unidentified)
- Recql5 (69 kDa, Protein from Homo sapiens)
- Template strand (8 kDa, DNA from unidentified)
- Transcription bubble rna strand (6 kDa, RNA from unidentified)
Human TFIID binds to core promoter DNA in a reorganized structural state
Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, Nogales E
Cell (2013) 152 pp. 120-131 [ Pubmed: 23332750 DOI: doi:10.1016/j.cell.2012.12.005 ]
- Holo-tfiid (canonical) (1 MDa, Sample)
- Transcription factor ii-d (1 MDa, Protein from Homo sapiens)
Structural visualization of key steps in human transcription initiation
He Y, Fang J, Taatjes DJ, Nogales E
Nature (2013) 495 pp. 481-486 [ Pubmed: 23446344 DOI: doi:10.1038/nature11991 ]
- Core promoter dna (55 kDa, DNA from Homo sapiens)
- General transcription factor iia (54 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (38 kDa, Protein from Homo sapiens)
- General transcription factor iib (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii (550 kDa, Protein from Homo sapiens)
- Tbp-tfiia-tfiib-dna-pol ii (close) (730 kDa, Sample)
Structural visualization of key steps in human transcription initiation
He Y, Fang J, Taatjes DJ, Nogales E
Nature (2013) 495 pp. 481-486 [ Pubmed: 23446344 DOI: doi:10.1038/nature11991 ]
- Core promoter dna (55 kDa, DNA from Homo sapiens)
- General transcription factor iif (87 kDa, Protein from Homo sapiens)
- General transcription factor iia (54 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (38 kDa, Protein from Homo sapiens)
- General transcription factor iib (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii (550 kDa, Protein from Homo sapiens)
- Tbp-tfiia-tfiib-dna-pol ii-tfiif (close) (820 kDa, Sample)
Structural visualization of key steps in human transcription initiation
He Y, Fang J, Taatjes DJ, Nogales E
Nature (2013) 495 pp. 481-486 [ Pubmed: 23446344 DOI: doi:10.1038/nature11991 ]
- Tbp-tfiia-tfiib-dna-pol ii-tfiif-tfiie (close) (900 kDa, Sample)
- Core promoter dna (55 kDa, DNA from Homo sapiens)
- General transcription factor iie (82 kDa, Protein from Homo sapiens)
- General transcription factor iif (87 kDa, Protein from Homo sapiens)
- General transcription factor iia (54 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (38 kDa, Protein from Homo sapiens)
- General transcription factor iib (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii (550 kDa, Protein from Homo sapiens)
Structural visualization of key steps in human transcription initiation
He Y, Fang J, Taatjes DJ, Nogales E
Nature (2013) 495 pp. 481-486 [ Pubmed: 23446344 DOI: doi:10.1038/nature11991 ]
- Tbp-tfiia-tfiib-dna-pol ii-tfiif-tfiie (open) (900 kDa, Sample)
- General transcription factor iie (82 kDa, Protein from Homo sapiens)
- General transcription factor iif (87 kDa, Protein from Homo sapiens)
- Core promoter dna (54 kDa, Macromolecule from Homo sapiens)
- General transcription factor iia (54 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (38 kDa, Protein from Homo sapiens)
- General transcription factor iib (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii (550 kDa, Protein from Homo sapiens)