Cryo-EM structure of the overlapping di-nucleosome (closed form)
Shimizu M, Tanaka H, Nishimura M, Sato N, Nozawa K, Ehara H, Sekine SI, Morishima K, Inoue R, Takizawa Y, Kurumizaka H, Sugiyama M
Pnas Nexus (2024) 3 pp. pgae484-pgae484 [ DOI: doi:10.1093/pnasnexus/pgae484 Pubmed: 39539301 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Overlapping di-nucleosome (Complex from Homo sapiens)
Cryo-EM structure of the overlapping di-nucleosome (intermediate form2)
Shimizu M, Tanaka H, Nishimura M, Sato N, Nozawa K, Ehara H, Sekine SI, Morishima K, Inoue R, Takizawa Y, Kurumizaka H, Sugiyama M
Pnas Nexus (2024) 3 pp. pgae484-pgae484 [ DOI: doi:10.1093/pnasnexus/pgae484 Pubmed: 39539301 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Overlapping di-nucleosome (Complex from Homo sapiens)
Cryo-EM structure of the overlapping di-nucleosome (open form)
Shimizu M, Tanaka H, Nishimura M, Sato N, Nozawa K, Ehara H, Sekine SI, Morishima K, Inoue R, Takizawa Y, Kurumizaka H, Sugiyama M
Pnas Nexus (2024) 3 pp. pgae484-pgae484 [ DOI: doi:10.1093/pnasnexus/pgae484 Pubmed: 39539301 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Overlapping di-nucleosome (Complex from Homo sapiens)
Resolution: 5.14 Å
EM Method: Single-particle
Fitted PDBs: 9dwu
Q-score: 0.122
Fisher RJ, Park K, Lee K, Pinjusic K, Vanasse A, Ennis CS, Ficcaro S, Marto J, Stransky S, Duke-Cohan J, Geethadevi A, Raabe E, Sidoli S, Hicks CW, Keskin DB, Wu CJ, Cole PA, Alani RM
bioRxiv (2024) [ Pubmed: 39713349 DOI: doi:10.1101/2024.12.12.627852 ]
- Lysine-specific histone demethylase 1a (74 kDa, Protein from Homo sapiens)
- Splicing factor u2af2 bound to the corest complex made up of lsd1 and rcor1 (Complex from Homo sapiens)
- Splicing factor u2af 65 kda subunit (8 kDa, Protein from Homo sapiens)
- Rest corepressor 1 (7 kDa, Protein from Homo sapiens)
P400 subcomplex of the native human TIP60 complex
Yang Z, Mameri A, Cattoglio C, Lachance C, Florez Ariza AJ, Luo J, Humbert J, Sudarshan D, Banerjea A, Galloy M, Fradet-Turcotte A, Lambert JP, Ranish JA, Cote J, Nogales E
Science (2024) 385 pp. eadl5816-eadl5816 [ Pubmed: 39088653 DOI: doi:10.1126/science.adl5816 ]
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Reconstituted p400 subcomplex of the human tip60 complex (Complex from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- E1a-binding protein p400 (343 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Histone h2b type 1-b (13 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Enhancer of polycomb homolog 1 (93 kDa, Protein from Homo sapiens)
Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 8jh2
Q-score: 0.145
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ Pubmed: 37981206 DOI: doi:10.1016/j.jbc.2023.105477 ]
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Homo sapiens)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histones (Complex from synthetic construct)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc27 (24 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*g)-3') (5 kDa, RNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
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 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (343-mer) (108 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna(343-mer) (109 kDa, DNA from synthetic construct)
- Isw1a-dinucleosome (392 MDa, Complex from Saccharomyces cerevisiae)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Iswi one complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae S288C)
Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome
Resolution: 5.6 Å
EM Method: Single-particle
Fitted PDBs: 7y61
Q-score: 0.189
Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM
Science (2023) 381 pp. eadd8673-eadd8673 [ DOI: doi:10.1126/science.add8673 Pubmed: 37616371 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Chromatin assembly factor 1 subunit b (46 kDa, Protein from Homo sapiens)
- Histone h4/h3.1 (Complex)
- Two caf1lcs bound right-handed di-tetrasome (Complex from Homo sapiens)
- Chromatin assembly factor 1 subunit a/b (Complex)
- Chromatin assembly factor 1 subunit a (47 kDa, Protein from Homo sapiens)
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 [ 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)
- Pic-mediator in complex with +1 nucleosome (t40n) in mh-binding state (Complex from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 14 (160 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 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)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- 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)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 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)
Nucleosome 2 of the 4x177 nucleosome array containing H1
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7pex
Q-score: 0.267
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Nucleosome 2 from 4x177 nucleosome array (Complex)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (177-mer) (55 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)