Cryo-EM structure of DDM1-nucleosome complex
Resolution: 4.71 Å
EM Method: Single-particle
Fitted PDBs: 8j90
Q-score: 0.243
Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H
Nat Commun (2024) 15 pp. 5187-5187 [ DOI: doi:10.1038/s41467-024-49465-w Pubmed: 38992002 ]
- Htb9 (16 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (51 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (87 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex (300 kDa, Complex from Arabidopsis thaliana)
- Hta6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j91
Q-score: 0.545
Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H
Nat Commun (2024) 15 pp. 5187-5187 [ DOI: doi:10.1038/s41467-024-49465-w Pubmed: 38992002 ]
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (51 kDa, DNA from synthetic construct)
- Hta13 (14 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Nucleosome containing arabidopsis thaliana histones (200 kDa, Complex from Arabidopsis thaliana)
Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j92
Q-score: 0.53
Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H
Nat Commun (2024) 15 pp. 5187-5187 [ DOI: doi:10.1038/s41467-024-49465-w Pubmed: 38992002 ]
- Htb9 (16 kDa, Protein from Arabidopsis thaliana)
- Nucleosome containing arabidopsis thaliana h2a.w (200 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (51 kDa, DNA from synthetic construct)
- Nucleosome (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Hta6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Dna (Complex)
Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T
EMBO J (2021) 40 [ Pubmed: 33463726 DOI: 10.15252/embj.2020105671 ]
Image sets:
Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T
EMBO J (2021) 40 [ Pubmed: 33463726 DOI: 10.15252/embj.2020105671 ]
Image sets:
Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T
EMBO J (2021) 40 [ Pubmed: 33463726 DOI: 10.15252/embj.2020105671 ]
Image sets:
Cryo-EM structure of the nucleosome containing Giardia histones
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 7d69
Q-score: 0.427
Sato S, Takizawa Y, Hoshikawa F, Dacher M, Tanaka H, Tachiwana H, Kujirai T, Iikura Y, Ho CH, Adachi N, Patwal I, Flaus A, Kurumizaka H
Nucleic Acids Res (2021) 49 pp. 8934-8946 [ DOI: doi:10.1093/nar/gkab644 Pubmed: 34352093 ]
- Histone h2b (14 kDa, Protein from Giardia intestinalis)
- 601l dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3 (16 kDa, Protein from Giardia intestinalis)
- Histone h4 (11 kDa, Protein from Giardia intestinalis)
- Nucleosome (Complex from Giardia intestinalis)
- 601l dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a (14 kDa, Protein from Giardia intestinalis)
The cryo-EM density map of CENP-A nucleosome in complex with CENP-C C-terminal domain
Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T
EMBO J (2021) 40 pp. e105671-e105671 [ DOI: doi:10.15252/embj.2020105671 Pubmed: 33463726 ]
Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T
EMBO J (2021) 40 pp. e105671-e105671 [ DOI: doi:10.15252/embj.2020105671 Pubmed: 33463726 ]
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7bxt
Q-score: 0.387
Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T
EMBO J (2021) 40 pp. e105671-e105671 [ DOI: doi:10.15252/embj.2020105671 Pubmed: 33463726 ]
- Histone h2b type 2-e (Complex from Escherichia coli (strain B / BL21-DE3))
- Cenp-c (4 kDa, Protein from Gallus gallus)
- Histone h4 (Complex from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (Complex from Homo sapiens)
- Cenp-c (Complex)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Maltodextrin-binding protein,centromere protein n (71 kDa, Protein from Gallus gallus)
- Maltodextrin-binding protein,centromere protein n (Complex)
- Histone h3,histone h3-like centromeric protein a (Complex from Homo sapiens)
- Histone h2b type 2-e (14 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Histone h3,histone h3-like centromeric protein a (16 kDa, Protein from Gallus gallus)
- Cenp-a nucleosome in complex with cenp-c peptide and cnep-n n-terminal domain (330 kDa, Complex from Ectocarpus siliculosus)