Structure of nucleosome complexed with two DEK molecules
Kujirai T, Echigoya K, Kishi Y, Saeki M, Ito T, Kato J, Negishi L, Ogasawara M, Kimura H, Masumoto H, Takizawa Y, Gotoh Y, Kurumizaka H
To Be Published
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Protein dek (43 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Dek dimer bound to the nucleosome (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
193 bp Widom601L nucleosome (closed)
Kujirai T, Echigoya K, Kishi Y, Saeki M, Ito T, Kato J, Negishi L, Kimura H, Masumoto H, Takizawa Y, Gotoh Y, Kurumizaka H
Nat Struct Mol Biol (2025) [ Pubmed: 39984731 DOI: doi:10.1038/s41594-025-01493-w ]
- 193 bp widom601l nucleosome (closed) (14 MDa, Complex from Homo sapiens)
193 bp Widom601L nucleosome (middle)
Kujirai T, Echigoya K, Kishi Y, Saeki M, Ito T, Kato J, Negishi L, Kimura H, Masumoto H, Takizawa Y, Gotoh Y, Kurumizaka H
Nat Struct Mol Biol (2025) [ Pubmed: 39984731 DOI: doi:10.1038/s41594-025-01493-w ]
- 193 bp widom601l nucleosome (closed) (14 MDa, Complex from Homo sapiens)
193 bp Widom601L nucleosome (open)
Kujirai T, Echigoya K, Kishi Y, Saeki M, Ito T, Kato J, Negishi L, Kimura H, Masumoto H, Takizawa Y, Gotoh Y, Kurumizaka H
Nat Struct Mol Biol (2025) [ Pubmed: 39984731 DOI: doi:10.1038/s41594-025-01493-w ]
- 193 bp widom601l nucleosome (open) (14 MDa, Complex from Homo sapiens)
Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome
Resolution: 4.52 Å
EM Method: Single-particle
Fitted PDBs: 8yny
Q-score: 0.218
Nagamura R, Kujirai T, Kato J, Shuto Y, Kusakizako T, Hirano H, Endo M, Toki S, Saika H, Kurumizaka H, Nureki O
Nat Commun (2024) 15 pp. 10744-10744 [ DOI: doi:10.1038/s41467-024-54768-z Pubmed: 39737984 ]
- Dna (17-mer) (5 kDa, DNA from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (175-mer) (53 kDa, DNA from Homo sapiens)
- Dna (176-mer) (54 kDa, DNA from Homo sapiens)
- Rna (97-mer) (31 kDa, RNA from Streptococcus pyogenes)
- Spcas9-sgrna-nucleosome ternary complex (Complex from Homo sapiens)
- 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 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)
Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8jla
Q-score: 0.453
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 h4 (10 kDa, Protein from Homo sapiens)
- Histone h3.1 (12 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (11 kDa, Protein from Homo sapiens)
- The human nucleosome lacking n-terminal region of h2a, h2b, h3, and h4 with scfv (Complex from Homo sapiens)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant
Resolution: 2.36 Å
EM Method: Single-particle
Fitted PDBs: 8jlb
Q-score: 0.602
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 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- The 145 bp human nucleosome containing h3.2 c110a mutant with scfv (Complex 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)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8jld
Q-score: 0.579
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 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- The 145 bp human nucleosome containing acetylated h3 tail with scfv (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I)
Resolution: 3.95 Å
EM Method: Single-particle
Fitted PDBs: 7w9v
Q-score: 0.307
Hatazawa S, Liu J, Takizawa Y, Zandian M, Negishi L, Kutateladze TG, Kurumizaka H
iScience (2022) 25 pp. 104563-104563 [ Pubmed: 35754730 DOI: doi:10.1016/j.isci.2022.104563 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone acetyltransferase p300 (74 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosome in complex with p300 acetyltransferase catalytic core (complex i) (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 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)