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)
Cryo-EM structure of the overlapping di-nucleosome (intermediate form1)
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: 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 h3.1 (15 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 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 nucleosome containing 193 base-pair DNA with a p53 target sequence
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 7xzy
Q-score: 0.256
Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H
Pnas Nexus (2022) 1 pp. pgac177-pgac177 [ DOI: doi:10.1093/pnasnexus/pgac177 Pubmed: 36714865 ]
- 193 base-pair dna (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone octamer (Complex)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Cryo-em structure of the nucleosome containing 193 base-pair dna with a p53 target sequence (239 kDa, 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)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7y00
Q-score: 0.32
Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H
Pnas Nexus (2022) 1 pp. pgac177-pgac177 [ DOI: doi:10.1093/pnasnexus/pgac177 Pubmed: 36714865 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- 169 base-pair of dna (Complex from Homo sapiens)
- Cryo-em structure of the nucleosome containing 169 base-pair dna with a p53 target sequence (223 kDa, Complex from Homo sapiens)
- Histone octamer (Complex)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain
Resolution: 4.53 Å
EM Method: Single-particle
Fitted PDBs: 7xzx
Q-score: 0.146
Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H
Pnas Nexus (2022) 1 pp. pgac177-pgac177 [ DOI: doi:10.1093/pnasnexus/pgac177 Pubmed: 36714865 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Cellular tumor antigen p53 (22 kDa, Protein from Homo sapiens)
- Cryo-em structure of the nucleosome in complex with p53 dna-binding domain (329 kDa, Complex from Homo sapiens)
- Nucleosome with p53 (Complex)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Dna (193-mer) (Complex)
- 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)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
Cryo-EM structure of the nucleosome in complex with p53
Resolution: 4.07 Å
EM Method: Single-particle
Fitted PDBs: 7xzz
Q-score: 0.192
Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H
Pnas Nexus (2022) 1 pp. pgac177-pgac177 [ DOI: doi:10.1093/pnasnexus/pgac177 Pubmed: 36714865 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Cellular tumor antigen p53 (43 kDa, Protein from Homo sapiens)
- Nucleosome, p53 (Complex)
- Cryo-em structure of the nucleosome in complex with p53 (398 kDa, Complex from Homo sapiens)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)