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 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)
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 8gui
Q-score: 0.532
Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T
Nat Commun (2024) 15 pp. 2580-2580 [ Pubmed: 38519511 DOI: doi:10.1038/s41467-024-46910-8 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Bre1-nucleosome complex (Complex)
- E3 ubiquitin-protein ligase bre1b (113 kDa, Protein from Homo sapiens)
- Bre1 (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone (Complex from Homo sapiens)
- Dna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase bre1a (113 kDa, Protein from Homo sapiens)
Human nucleosome core particle (free form)
Resolution: 2.51 Å
EM Method: Single-particle
Fitted PDBs: 8guk
Q-score: 0.588
Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T
Nat Commun (2024) 15 pp. 2580-2580 [ Pubmed: 38519511 DOI: doi:10.1038/s41467-024-46910-8 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Hiistone (Complex)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex)
- Bre1-nucleosome complex (Complex from Homo sapiens)
Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence
Resolution: 1.89 Å
EM Method: Single-particle
Fitted PDBs: 7vz4
Q-score: 0.724
Takizawa Y, Ho CH, Sato S, Danev R, Kurumizaka H
To Be Published
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Human nucleosome core particle composed of the widom 601l dna sequence (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)