Cryo-EM structure of ISW1a-dinucleosome
Resolution: 5.4 Å
EM Method: Single-particle
Fitted PDBs: 7x3t
Q-score: 0.192
Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z
Nat Struct Mol Biol (2024) 31 pp. 266-274 [ DOI: doi:10.1038/s41594-023-01174-6 Pubmed: 38177688 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Iswi one complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (343-mer) (108 kDa, DNA from synthetic construct)
- Isw1a-dinucleosome (392 MDa, Complex from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna(343-mer) (109 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state
Resolution: 5.04 Å
EM Method: Single-particle
Fitted PDBs: 8gxq
Q-score: 0.084
Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y
Science (2022) 378 pp. 62-68 [ Pubmed: 36201575 DOI: doi:10.1126/science.abn8131 ]
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 1 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- 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)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Dna (162-mer) (53 kDa, DNA from synthetic construct)
- Transcription initiation factor tfiid subunit 8 (34 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)
- 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)
- 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)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 26 (65 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 11 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Pic-mediator in complex with +1 nucleosome (t40n) in mh-binding state (Complex from Sus scrofa)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- 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)
- Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Dna (228-mer) (70 kDa, DNA from synthetic construct)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Dna (162-mer) (46 kDa, DNA from synthetic construct)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 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 14 (160 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 29 (21 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 3 (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna (228-mer) (70 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 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 tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- 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)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome.
Finogenova K, Bonnet J, Poepsel S, Schafer IB, Finkl K, Schmid K, Litz C, Strauss M, Benda C, Muller J
eLife (2020) 9 [ DOI: doi:10.7554/eLife.61964 Pubmed: 33211010 ]
- Histone h3.2 (Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase ezh2, polycomb protein eed, polycomb protein suz12 (Complex from Homo sapiens)
- Polycomb protein suz12 (Protein from Homo sapiens)
- Histone h2b (Protein from Xenopus laevis)
- Widom601 dna + linker (Complex from synthetic construct)
- Polycomb protein eed (Protein from Homo sapiens)
- Histone h2a (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Widom601 dna + linker (RNA from synthetic construct)
- Cryo-em map of phf1-prc2 on a heterodimeric dinucleosome (Complex)
- Histone-lysine n-methyltransferase ezh2 (Protein from Homo sapiens)
Nucleosome breathing : Class 2
Resolution: 5.4 Å
EM Method: Single-particle
Fitted PDBs: 6esg
Q-score: 0.198
Bilokapic S, Strauss M, Halic M
Nat Struct Mol Biol (2018) 25 pp. 101-108 [ DOI: doi:10.1038/s41594-017-0005-5 Pubmed: 29323273 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (141-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nucleosome (200 kDa, Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (141-mer) (45 kDa, DNA from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Dna (Complex from Synthetic construct)
Nucleosome breathing : Class 3
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 6esh
Q-score: 0.209
Bilokapic S, Strauss M, Halic M
Nat Struct Mol Biol (2018) 25 pp. 101-108 [ DOI: doi:10.1038/s41594-017-0005-5 Pubmed: 29323273 ]
- Dna (Complex from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
- Nucleosome (200 kDa, Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
- Nucleosome (Complex from Xenopus laevis)