RNA polymerase II core pre-initiation complex focused map
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798-1809.e7 [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
Dimerized Mediator-PIC with early GTFs and TFIIE on a divergent promoter
Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023) 83 pp. 574-588.e11 [ DOI: doi:10.1016/j.molcel.2023.01.011 Pubmed: 36731470 ]
Dimerized Mediator PIC with early GTFs on a divergent promoter
Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023) 83 pp. 574-588.e11 [ DOI: doi:10.1016/j.molcel.2023.01.011 Pubmed: 36731470 ]
Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7zx8
Q-score: 0.356
Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ DOI: doi:10.1038/s41594-022-00857-w Pubmed: 36424526 ]
- Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
- Template strand (29 kDa, DNA from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Promoter (Complex from Sus scrofa)
- Snapc (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Pre-initiation complex of rna polymerase ii with general transcription factors and snapc bound to u1 promoter (Complex)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Snrna-activating protein complex subunit 5 (11 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Non-template strand (29 kDa, DNA from Homo sapiens)
Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7zwc
Q-score: 0.452
Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ DOI: doi:10.1038/s41594-022-00857-w Pubmed: 36424526 ]
- General transcription factors and snapc bound to u5 promoter (Complex)
- Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 5 (11 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Non-template strand (29 kDa, DNA from Homo sapiens)
- Snapc (Complex from Homo sapiens)
- Template strand (29 kDa, DNA from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Promoter (Complex from Homo sapiens)
Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7zwd
Q-score: 0.342
Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ DOI: doi:10.1038/s41594-022-00857-w Pubmed: 36424526 ]
- Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Promoter (Complex from Sus scrofa)
- Non-template strand (29 kDa, DNA from Homo sapiens)
- Snapc (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Pre-initiation complex of rna polymerase ii with general transcription factors and snapc bound to u5 promoter (Complex)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Template strand (29 kDa, DNA from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Snrna-activating protein complex subunit 5 (11 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7zx7
Q-score: 0.267
Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ DOI: doi:10.1038/s41594-022-00857-w Pubmed: 36424526 ]
- Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
- Template strand (29 kDa, DNA from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Snapc (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Pre-initiation complex of rna polymerase ii with general transcription factors and snapc bound to u1 promoter (Complex)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Snrna-activating protein complex subunit 5 (11 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Non-template strand (29 kDa, DNA from Homo sapiens)
- Promoter (Complex from Homo sapiens)
Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7zxe
Q-score: 0.333
Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 1159-1169 [ DOI: doi:10.1038/s41594-022-00857-w Pubmed: 36424526 ]
- Tata-box-binding protein and transcription factors (Complex from Homo sapiens)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Template strand (29 kDa, DNA from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 5 (11 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- General transcription factors and snapc bound to u1 promoter (Complex)
- Snapc (Complex from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Non-template strand (29 kDa, DNA from Homo sapiens)
- Promoter (Complex from Homo sapiens)
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 [ Pubmed: 33707221 DOI: doi:10.1126/science.abg3074 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Tfiih (500 kDa, Complex from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 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)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Homo sapiens)
- Rna polymerase ii (520 kDa, Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 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 15 (86 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 rpb2 (134 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Super core promoter antisense strand (30 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Super core promoter sense strand (31 kDa, DNA from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Promoter dna (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Mediator-bound pre-initiation complex (2 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- General transcription factors (300 kDa, Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 22 (22 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)
- Iron/sulfur cluster (351 Da, Ligand)
- Cyclin-h and associated factors (Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
Focused refinement on the cPIC within the human Mediator-bound transcription pre-initiation complex
Abdella R, Talyzina A, Chen S, Inouye CJ, Tjian R, He Y
Science (2021) 372 pp. 52-56 [ Pubmed: 33707221 DOI: doi:10.1126/science.abg3074 ]
- Mediator (1 MDa, Complex from Homo sapiens)
- General transcription factors (300 kDa, Complex from Homo sapiens)
- Tfiih (500 kDa, Complex from Homo sapiens)
- Promoter dna (Complex from Homo sapiens)
- Rna polymerase ii (520 kDa, Complex from Homo sapiens)
- Mediator-bound pre-initiation complex (Complex)