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 h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Dna (250-mer) (77 kDa, DNA from synthetic construct)
- Overlapping di-nucleosome (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein 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 h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Dna (250-mer) (77 kDa, DNA from synthetic construct)
- Overlapping di-nucleosome (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein 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 h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Dna (250-mer) (77 kDa, DNA from synthetic construct)
- Overlapping di-nucleosome (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein 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) [ DOI: doi:10.1101/2024.12.12.627852 Pubmed: 39713349 ]
- Rest corepressor 1 (7 kDa, Protein from Homo sapiens)
- Splicing factor u2af2 bound to the corest complex made up of lsd1 and rcor1 (Complex from Homo sapiens)
- Lysine-specific histone demethylase 1a (74 kDa, Protein from Homo sapiens)
- Splicing factor u2af 65 kda subunit (8 kDa, Protein from Homo sapiens)
Locally refined map for Nap1 and H2A-H2B in (Nap1)2-H2A-H2B-Kap114 structure
Fung HYJ, Jiou J, Niesman AB, Bernardes NE, Chook YM
J Cell Biol (2025) 224 [ DOI: doi:10.1083/jcb.202408193 Pubmed: 39601790 ]
Medusavirus Nucleosome Core Particle Native
Toner CM, Hoitsma NM, Weerawarana S, Luger K
Nat Commun (2024) 15 pp. 9138-9138 [ DOI: doi:10.1038/s41467-024-53364-5 Pubmed: 39443461 ]
- Widom 601 dna (Complex from synthetic construct)
- Widom 601 dna (207 mer) strand 1 (DNA from synthetic construct)
- Histone h2b (Protein from Medusavirus medusae)
- Histone complex (Complex from Medusavirus)
- Histone h3 (Protein from Medusavirus medusae)
- Histone h4 (Protein from Medusavirus medusae)
- Medusavirus nucleosome core particle (Complex)
- Widom 601 dna (207 mer) strand 2 (DNA from synthetic construct)
- Histone h2a (Protein from Medusavirus medusae)
Cryo-EM density map of DNMT3A1-DNMT3L on a human H2AKc119ub nucleosome at 5.1 A resolution
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Histone h2ak119c (Protein from Homo sapiens)
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Histone h3 (Protein from Homo sapiens)
- Dnmt3a1 (Protein from Homo sapiens)
- Dnmt3l (Protein from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- 195bp widom601 dna (DNA from synthetic construct)
- Ubiquitin (Protein from Homo sapiens)
- Histone h2b (Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex 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 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- E1a-binding protein p400 (343 kDa, Protein from Homo sapiens)
- Enhancer of polycomb homolog 1 (93 kDa, Protein from Homo sapiens)
- Reconstituted p400 subcomplex of the human tip60 complex (Complex from Homo sapiens)
- Histone h2b type 1-b (13 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 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 [ DOI: doi:10.1016/j.jbc.2023.105477 Pubmed: 37981206 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Transcription elongation factor 1 homolog (12 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)
- Rna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc27 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Homo sapiens)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)