Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8ybj
Q-score: 0.631
Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H
Genes Cells (2024) 29 pp. 769-781 [ Pubmed: 38972377 DOI: doi:10.1111/gtc.13143 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- The human nucleosome containing h3.1 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 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)
Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8ybk
Q-score: 0.598
Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H
Genes Cells (2024) 29 pp. 769-781 [ Pubmed: 38972377 DOI: doi:10.1111/gtc.13143 ]
- The human nucleosome containing h3.1 e97k mutant (Complex from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8jnd
Q-score: 0.19
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
Resolution: 4.68 Å
EM Method: Single-particle
Fitted PDBs: 8jne
Q-score: 0.13
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
The cryo-EM structure of the RAD51 filament bound to the nucleosome
Resolution: 6.91 Å
EM Method: Single-particle
Fitted PDBs: 8jnf
Q-score: 0.143
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 8xbt
Q-score: 0.199
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
Resolution: 4.24 Å
EM Method: Single-particle
Fitted PDBs: 8xbu
Q-score: 0.171
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
Resolution: 7.64 Å
EM Method: Single-particle
Fitted PDBs: 8ihl
Q-score: 0.109
Nishimura M, Fujii T, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y, Kurumizaka H
Commun Biol (2024) 7 pp. 61-61 [ DOI: doi:10.1038/s42003-023-05694-1 Pubmed: 38191828 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (353-mer) (108 kDa, DNA from synthetic construct)
- Overlapping tri-nucleosome (511 kDa, Complex from Homo sapiens)
- Dna (353-mer) (109 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)
Cryo-EM structure of the human nucleosome containing H3.8
Resolution: 2.26133 Å
EM Method: Single-particle
Fitted PDBs: 8kb5
Q-score: 0.655
Hirai S, Kujirai T, Akatsu M, Ogasawara M, Ehara H, Sekine SI, Ohkawa Y, Takizawa Y, Kurumizaka H
J.Biochem. (2023) 174 pp. 549-559 [ Pubmed: 37757444 DOI: doi:10.1093/jb/mvad069 ]
- Histone h3.8 (16 kDa, Protein from Homo sapiens)
- The human nucleosome containing h3.8 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human nucleosome with scFv
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8jl9
Q-score: 0.569
Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H
Nucleic Acids Res (2023) 51 pp. 10364-10374 [ DOI: doi:10.1093/nar/gkad754 Pubmed: 37718728 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Dna (193-mer) (59 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)
- The 193 bp human nucleosome with scfv (Complex from Homo sapiens)