RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- General transcription factor iib (Complex 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)
- 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)
- Tata-box binding protein (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription factor iia (Complex from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- 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 ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- Cyclin-h (37 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)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iif (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iie (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- 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)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
Human Mediator with RNA Polymerase II Pre-initiation complex
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7nvr
Q-score: 0.171
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 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)
- 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)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Unassigned peptides (med29 or med30) (Complex from Trichoplusia ni)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (89 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)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Homo sapiens)
- Unassigned peptide (med6) (1 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 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)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Nt (32 kDa, DNA from Human mastadenovirus C)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Unassigned peptide (med17) (954 Da, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Template (32 kDa, DNA from Human mastadenovirus C)
- Unassigned peptide (med14) (1 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 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)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Transcription initiation factors (Complex from Homo sapiens)
- Human mediator with rna polymerase ii pre-initiation complex (Complex)
- Nt and template (Complex from Human mastadenovirus C)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 19 (26 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)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Pol complex and mediator of rna polymerase ii transcription (Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 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)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nvv
Q-score: 0.499
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ DOI: doi:10.1038/s41586-021-03554-8 Pubmed: 33902107 ]
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- General transcription factor iie subunit 1 (49 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 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Xpb-containing part of tfiih (150 kDa, Complex)
- Adenosine-5'-diphosphate (427 Da, Ligand)
TFIIH in a pre-translocated state (without ADP-BeF3)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7nvw
Q-score: 0.279
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Tfiih (without adp-bef3) (490 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
TFIIH in a post-translocated state (with ADP-BeF3)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7nvx
Q-score: 0.305
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Tfiih (with adp-bef3) (490 kDa, Complex)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
Resolution: 7.3 Å
EM Method: Single-particle
Fitted PDBs: 7nvy
Q-score: 0.118
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein 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)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- 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)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- 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_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- 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)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Rna polymerase ii pre-initiation complex with closed promoter dna in proximal position (1 MDa, Complex)
RNA polymerase II pre-initiation complex with closed promoter DNA in distal position
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 7nvz
Q-score: 0.111
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with closed promoter dna in distal position (1 MDa, Complex)
- 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)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- 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)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- 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_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- 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)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
RNA polymerase II pre-initiation complex with open promoter DNA
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 7nw0
Q-score: 0.119
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 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)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- 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)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with open promoter dna (1 MDa, Complex)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- 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_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- 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)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
Architecture of the yeast small subunit processome
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 5tzs
Q-score: 0.222
Chaker-Margot M, Barandun J, Hunziker M, Klinge S
Science (2017) 355 [ Pubmed: 27980088 DOI: doi:10.1126/science.aal1880 ]
- Repeat protein 2 (31 kDa, Protein from Saccharomyces cerevisiae S288c)
- 5' external transcribed spacer (72 kDa, RNA from Saccharomyces cerevisiae S288c)
- Utp6 (26 kDa, Protein from Saccharomyces cerevisiae S288c)
- Nop1 (18 kDa, Protein from Saccharomyces cerevisiae S288c)
- 13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Utpa_ctd4 (8 kDa, Protein from Saccharomyces cerevisiae S288c)
- Utpa_ctd1 (14 kDa, Protein from Saccharomyces cerevisiae S288c)
- Unassigned rna helices (14 kDa, DNA from Saccharomyces cerevisiae S288c)
- Utp4 (46 kDa, Protein from Saccharomyces cerevisiae S288c)
- Beta-propeller 5 (24 kDa, Protein from Saccharomyces cerevisiae S288c)
- Utp13 (61 kDa, Protein from Saccharomyces cerevisiae S288c)
- 3' domain-associated (21 kDa, DNA from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beta-propeller 2 (21 kDa, Protein from Saccharomyces cerevisiae S288c)
- 5' domain-associated (7 kDa, DNA from Saccharomyces cerevisiae S288c)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nop58 (29 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- U3 snorna (37 kDa, RNA from Saccharomyces cerevisiae S288c)
- Ribosomal rna-processing protein 9 (65 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ribosomal rna small subunit methyltransferase nep1 (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Utp30 (13 kDa, Protein from Saccharomyces cerevisiae S288c)
- Unassigned protein helices (43 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- Enp2 (22 kDa, Protein from Saccharomyces cerevisiae S288c)
- Kre33 (54 kDa, Protein from Saccharomyces cerevisiae S288c)
- Utp18 (21 kDa, Protein from Saccharomyces cerevisiae S288c)
- Imp3 (12 kDa, Protein from Saccharomyces cerevisiae S288c)
- Unassigned kh domain (14 kDa, Protein from Saccharomyces cerevisiae S288c)
- Small subunit processome (4 MDa, Complex from Saccharomyces cerevisiae S288c)
- Repeat protein 1 (49 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Utp20 (78 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Utp12 (60 kDa, Protein from Saccharomyces cerevisiae S288c)
- Kre33 (54 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Utp24 (10 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Utpa_ctd2 (9 kDa, Protein from Saccharomyces cerevisiae S288c)
- Utp1 (54 kDa, Protein from Saccharomyces cerevisiae S288c)
- U3 small nucleolar rna-associated protein 21,utp21 (83 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nop1 (18 kDa, Protein from Saccharomyces cerevisiae S288c)
- Beta-propeller 1 (24 kDa, Protein from Saccharomyces cerevisiae S288c)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Utp17 (46 kDa, Protein from Saccharomyces cerevisiae S288c)
- Nop56 (26 kDa, Protein from Saccharomyces cerevisiae S288c)
- Bms1,ribosome biogenesis protein bms1,bms1,ribosome biogenesis protein bms1 (46 kDa, Protein from Saccharomyces cerevisiae S288c)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae S288C)
- Imp4 (13 kDa, Protein from Saccharomyces cerevisiae S288c)