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 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 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)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iie (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- General transcription factor iib (Complex from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
structure of C2 projections and MIPs
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7n61
Q-score: 0.405
Han L, Rao Q, Yang R, Wang Y, Chai P, Xiong Y, Zhang K
Nat Struct Mol Biol (2022) 29 pp. 472-482 [ DOI: doi:10.1038/s41594-022-00769-9 Pubmed: 35578022 ]
- Unassigned protein-2 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Kinesin-like protein (83 kDa, Protein from Chlamydomonas reinhardtii)
- Fap147 (102 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin beta (49 kDa, Protein from Chlamydomonas reinhardtii)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Unassigned protein-5 (7 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Unassigned protein-4 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Structure of c2 projections and mips (Complex from Chlamydomonas reinhardtii)
- Unassigned protein-1 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Fap65 (233 kDa, Protein from Chlamydomonas reinhardtii)
- Fap70 (111 kDa, Protein from Chlamydomonas reinhardtii)
- Fap239 (57 kDa, Protein from Chlamydomonas reinhardtii)
- Fap213 (22 kDa, Protein from Chlamydomonas reinhardtii)
- Unassigned protein-3 (13 kDa, Protein from Chlamydomonas reinhardtii)
- Fap225 (81 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar wd repeat-containing protein pf20 (65 kDa, Protein from Chlamydomonas reinhardtii)
- Unassigned protein-6 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Fap178 (23 kDa, Protein from Chlamydomonas reinhardtii)
- Fap196 (64 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin alpha (49 kDa, Protein from Chlamydomonas reinhardtii)
cryo-EM structure of transcription coactivator SAGA
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6t9i
Q-score: 0.38
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ DOI: doi:10.1038/s41586-020-1933-5 Pubmed: 31969703 ]
- Transcription initiation factor tfiid subunit 12 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unassigned sequence (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor tfiid subunit 6 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional activator spt7 (152 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional coactivator hfi1/ada1 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 5 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor spt20 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga complex (1 MDa, Complex from Saccharomyces cerevisiae S288C)
- Saga-associated factor 73 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein spt3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6t9k
Q-score: 0.473
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ DOI: doi:10.1038/s41586-020-1933-5 Pubmed: 31969703 ]
- Transcription initiation factor tfiid subunit 12 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga core module (500 kDa, Complex from Saccharomyces cerevisiae S288C)
- Unassigned sequence (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor tfiid subunit 6 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional activator spt7 (152 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional coactivator hfi1/ada1 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor spt20 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 5 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga-associated factor 73 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein spt3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)
Resolution: 8.7 Å
EM Method: Single-particle
Fitted PDBs: 5wyj
Q-score: 0.16
Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K
eLife (2017) 6 [ Pubmed: 28244370 DOI: doi:10.7554/eLife.22086 ]
- Enp2 (60 kDa, Protein from Baker's yeast)
- 90s small subunit pre-ribosome (dhr1-depleted, enp1-tap) (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s28-a (7 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s24-a (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s5 (25 kDa, Protein from Baker's yeast)
- Rrna biogenesis protein rrp5 (193 kDa, Protein from Baker's yeast)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s8-a (22 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s27-a (8 kDa, Protein from Baker's yeast)
- Ribosomal rna small subunit methyltransferase nep1 (27 kDa, Protein from Baker's yeast)
- Nucleolar protein 56 (56 kDa, Protein from Baker's yeast)
- Helical domain protein (137 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s1-a (28 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s11-a (17 kDa, Protein from Baker's yeast)
- Ribosomal rna-processing protein 7 (34 kDa, Protein from Baker's yeast)
- Utp9 (48 kDa, Protein from Baker's yeast)
- Ribosomal rna-processing protein 9 (65 kDa, Protein from Baker's yeast)
- Ubiquitin-40s ribosomal protein s31 (17 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s16-a (15 kDa, Protein from Baker's yeast)
- Essential nuclear protein 1 (55 kDa, Protein from Baker's yeast)
- Rrna-processing protein fcf1 (21 kDa, Protein from Baker's yeast)
- Unassigned helices (87 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 18 (66 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 21 (104 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 22 (140 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 13 (91 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s6-a (27 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s14-a (14 kDa, Protein from Baker's yeast)
- Helical domain protein (84 kDa, Protein from Baker's yeast)
- Utp15 (43 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein bms1 (135 kDa, Protein from Baker's yeast)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Baker's yeast)
- Mpp10,u3 small nucleolar rna-associated protein mpp10 (54 kDa, Protein from Baker's yeast)
- Utp4 (66 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s22-a (14 kDa, Protein from Baker's yeast)
- Sof1 (41 kDa, Protein from Baker's yeast)
- Rrna 2'-o-methyltransferase fibrillarin (34 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s4-a (29 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein utp30 (31 kDa, Protein from Baker's yeast)
- Utp7 (47 kDa, Protein from Baker's yeast)
- Utp17 (76 kDa, Protein from Baker's yeast)
- Pre-rrna-processing protein pno1 (30 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 10,utp10 (173 kDa, Protein from Baker's yeast)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s23-a (16 kDa, Protein from Baker's yeast)
- 18s ribosomal rna (583 kDa, RNA from Baker's yeast)
- 13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s30-a (7 kDa, Protein from Baker's yeast)
- Utp11 (21 kDa, Protein from Baker's yeast)
- 5ets rna (225 kDa, RNA from Baker's yeast)
- Periodic tryptophan protein 2 (104 kDa, Protein from Baker's yeast)
- Nucleolar protein 58 (57 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s7-a (21 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s12 (15 kDa, Protein from Baker's yeast)
- Utp20 (212 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s9-a (22 kDa, Protein from Baker's yeast)
- U3 rna (106 kDa, RNA from Baker's yeast)
- 40s ribosomal protein s13 (17 kDa, Protein from Baker's yeast)
- Utp8 (60 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 12 (106 kDa, Protein from Baker's yeast)
- Utp5 (54 kDa, Protein from Baker's yeast)
- Krr1 small subunit processome component (37 kDa, Protein from Baker's yeast)
Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 5wyk
Q-score: 0.267
Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K
eLife (2017) 6 [ Pubmed: 28244370 DOI: doi:10.7554/eLife.22086 ]
- Enp2 (60 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s28-a (7 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s24-a (15 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s5 (25 kDa, Protein from Baker's yeast)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s8-a (22 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s27-a (8 kDa, Protein from Baker's yeast)
- Ribosomal rna small subunit methyltransferase nep1 (27 kDa, Protein from Baker's yeast)
- Nucleolar protein 56 (56 kDa, Protein from Baker's yeast)
- Helical domain protein (137 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 10 (200 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s1-a (28 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s11-a (17 kDa, Protein from Baker's yeast)
- Ribosomal rna-processing protein 7 (34 kDa, Protein from Baker's yeast)
- Utp9 (48 kDa, Protein from Baker's yeast)
- Ribosomal rna-processing protein 9 (65 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s16-a (15 kDa, Protein from Baker's yeast)
- Rrna-processing protein fcf1 (21 kDa, Protein from Baker's yeast)
- Unassigned helices (87 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 18 (66 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 21 (104 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 22 (140 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 13 (91 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s14-a (14 kDa, Protein from Baker's yeast)
- Helical domain protein (84 kDa, Protein from Baker's yeast)
- Utp15 (43 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein bms1 (135 kDa, Protein from Baker's yeast)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Baker's yeast)
- 90s small subunit pre-ribosome (mtr4-depleted, enp1-tap) (Complex from Saccharomyces cerevisiae)
- Utp4 (66 kDa, Protein from Baker's yeast)
- Mpp10,u3 small nucleolar rna-associated protein mpp10 (54 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s22-a (14 kDa, Protein from Baker's yeast)
- Sof1 (41 kDa, Protein from Baker's yeast)
- Rrna 2'-o-methyltransferase fibrillarin (34 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s4-a (29 kDa, Protein from Baker's yeast)
- Ribosome biogenesis protein utp30 (31 kDa, Protein from Baker's yeast)
- Utp7 (47 kDa, Protein from Baker's yeast)
- Utp17 (76 kDa, Protein from Baker's yeast)
- Pre-rrna-processing protein pno1 (30 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s23-a (16 kDa, Protein from Baker's yeast)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Baker's yeast)
- 18s ribosomal rna (583 kDa, RNA from Baker's yeast)
- 13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s30-a (7 kDa, Protein from Baker's yeast)
- Utp11 (21 kDa, Protein from Baker's yeast)
- 5ets rna (225 kDa, RNA from Baker's yeast)
- Periodic tryptophan protein 2 (104 kDa, Protein from Baker's yeast)
- Nucleolar protein 58 (57 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s7-a (21 kDa, Protein from Baker's yeast)
- 40s ribosomal protein s9-a (22 kDa, Protein from Baker's yeast)
- U3 rna (106 kDa, RNA from Baker's yeast)
- 40s ribosomal protein s13 (17 kDa, Protein from Baker's yeast)
- Utp8 (60 kDa, Protein from Baker's yeast)
- U3 small nucleolar rna-associated protein 12 (106 kDa, Protein from Baker's yeast)
- Utp5 (54 kDa, Protein from Baker's yeast)
- Krr1 small subunit processome component (37 kDa, Protein from Baker's yeast)