Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex)
Resolution: 3.82 Å
EM Method: Single-particle
Fitted PDBs: 9j8m
Q-score: 0.345
Horikoshi N, Miyake R, Sogawa-Fujiwara C, Ogasawara M, Takizawa Y, Kurumizaka H
Nat Commun (2025) 16 pp. 1495-1495 [ DOI: doi:10.1038/s41467-025-56823-9 Pubmed: 39929866 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Lamin-a/c (17 kDa, Protein from Homo sapiens)
- High mobility complex containing baf, lamin a/c igf, and nucleosome (270 kDa, Complex from Homo sapiens)
- Barrier-to-autointegration factor (10 kDa, Protein from Homo sapiens)
- 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)
Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex)
Resolution: 7.14 Å
EM Method: Single-particle
Fitted PDBs: 9j8n
Q-score: 0.164
Horikoshi N, Miyake R, Sogawa-Fujiwara C, Ogasawara M, Takizawa Y, Kurumizaka H
Nat Commun (2025) 16 pp. 1495-1495 [ DOI: doi:10.1038/s41467-025-56823-9 Pubmed: 39929866 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Lamin-a/c (17 kDa, Protein from Homo sapiens)
- Barrier-to-autointegration factor (10 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Low mobility complex containing baf, lamin a/c igf, and nucleosome (620 kDa, 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 BAF-Lamin A/C IgF-H1-nucleosome complex
Resolution: 4.05 Å
EM Method: Single-particle
Fitted PDBs: 9j8o
Q-score: 0.292
Horikoshi N, Miyake R, Sogawa-Fujiwara C, Ogasawara M, Takizawa Y, Kurumizaka H
Nat Commun (2025) 16 pp. 1495-1495 [ DOI: doi:10.1038/s41467-025-56823-9 Pubmed: 39929866 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Complex containing baf, lamin a/c igf, h1, and nucleosome (580 kDa, Complex from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Lamin-a/c (17 kDa, Protein from Homo sapiens)
- Barrier-to-autointegration factor (10 kDa, Protein from Homo sapiens)
- Histone h1.1 (22 kDa, Protein from Homo sapiens)
- 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)
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 h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 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)
- Overlapping di-nucleosome (Complex 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 h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 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)
- Overlapping di-nucleosome (Complex 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 h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 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)
- Overlapping di-nucleosome (Complex 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 h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (250-mer) (77 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)
- Overlapping di-nucleosome (Complex from Homo sapiens)
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)
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)