The structure of INTAC-PEC complex
Resolution: 4.18 Å
EM Method: Single-particle
Fitted PDBs: 7ycx
Q-score: 0.311
Zheng H, Jin Q, Wang X, Qi Y, Liu W, Ren Y, Zhao D, Xavier Chen F, Cheng J, Chen X, Xu Y
Protein Cell (2023) 14 pp. 698-702 [ Pubmed: 36869814 DOI: doi:10.1093/procel/pwad010 ]
- Intac (Complex from Sus scrofa)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit (Complex)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna (7 kDa, RNA from synthetic construct)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1,dna-directed rna polymerase ii subunit rpb1, ctd1, ctd2, ctd3, ctd4 (217 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Intac-pec (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Template dna (14 kDa, DNA from synthetic construct)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna/rna (Complex)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Unknown2 (1 kDa, Protein from Homo sapiens)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
Resolution: 4.16 Å
EM Method: Single-particle
Fitted PDBs: 8gxs
Q-score: 0.093
Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y
Science (2022) 378 pp. 62-68 [ DOI: doi:10.1126/science.abn8131 Pubmed: 36201575 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 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 rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (228-mer) (70 kDa, DNA from synthetic construct)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- Pic-mediator in complex with +1 nucleosome (t40n) in h-binding state (Complex from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- Dna (162-mer) (46 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 7 (39 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)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna (228-mer) (70 kDa, DNA from synthetic construct)
- Mediator of rna polymerase ii transcription subunit 26 (65 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna (162-mer) (53 kDa, DNA from synthetic construct)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 1 (168 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
p53-bound TFIID-based core PIC on HDM2 promoter
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7edx
Q-score: 0.13
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Tfiib (Complex 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)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna(scp promoters) (Complex)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Dna (84-mer) (26 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- P53-bound tfiid-based core pic on hdm2 promoter (Complex)
- Dna (84-mer) (25 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
TFIID-based intermediate PIC on PUMA promoter
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7ega
Q-score: 0.122
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit (167 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Tfiib (Complex 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)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Dna(puma promoters) (Complex)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Tfiid-based intermediate pic on puma promoter (Complex)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)