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 [ Pubmed: 38992002 DOI: doi:10.1038/s41467-024-49465-w ]
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Ddm1-nucleosome complex (300 kDa, Complex from Arabidopsis thaliana)
- Hta6 (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)
- Htb9 (16 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
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 [ Pubmed: 38992002 DOI: doi:10.1038/s41467-024-49465-w ]
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Hta13 (14 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Nucleosome containing arabidopsis thaliana histones (200 kDa, Complex from Arabidopsis thaliana)
- Dna (169-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein 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 [ Pubmed: 38992002 DOI: doi:10.1038/s41467-024-49465-w ]
- Dna (Complex)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Hta6 (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)
- Htb9 (16 kDa, Protein from Arabidopsis thaliana)
- Nucleosome (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8jg5
Q-score: 0.376
Kimura-Someya T, Katsura K, Kato-Murayama M, Hosaka T, Uchikubo-Kamo T, Ihara K, Hanada K, Sato S, Murayama K, Kataoka M, Shirouzu M, Someya Y
J Virol (2024) 98 pp. e0019724-e0019724 [ DOI: doi:10.1128/jvi.00197-24 Pubmed: 38593321 ]
- Viral protein 1 with its antibody fragments (Complex from Chiba virus)
- Vl,sarah (18 kDa, Protein from Homo sapiens)
- Vp1 (58 kDa, Protein from Chiba virus)
- Vh,sarah (19 kDa, Protein 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 h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Human nucleosome core particle composed of the widom 601l dna sequence (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8hag
Q-score: 0.29
Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T
Nat Commun (2023) 14 pp. 4103-4103 [ Pubmed: 37460559 DOI: doi:10.1038/s41467-023-39735-4 ]
- Histone acetyltransferase p300 (92 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (180-mer) (55 kDa, DNA from Homo sapiens)
- The p300 catalytic core bound to the h4k12ack16ac nucleosome (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)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8hah
Q-score: 0.159
Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T
Nat Commun (2023) 14 pp. 4103-4103 [ Pubmed: 37460559 DOI: doi:10.1038/s41467-023-39735-4 ]
- Histone acetyltransferase p300 (92 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (180-mer) (55 kDa, DNA from Homo sapiens)
- The p300 catalytic core bound to the h4k12ack16ac nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T
Nat Commun (2023) 14 pp. 4103-4103 [ Pubmed: 37460559 DOI: doi:10.1038/s41467-023-39735-4 ]
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 8hai
Q-score: 0.212
Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T
Nat Commun (2023) 14 pp. 4103-4103 [ Pubmed: 37460559 DOI: doi:10.1038/s41467-023-39735-4 ]
- Histone acetyltransferase p300 (92 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (180-mer) (55 kDa, DNA from Homo sapiens)
- The p300 catalytic core bound to the h4k12ack16ac nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 8haj
Q-score: 0.2
Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T
Nat Commun (2023) 14 pp. 4103-4103 [ Pubmed: 37460559 DOI: doi:10.1038/s41467-023-39735-4 ]
- Histone acetyltransferase p300 (92 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (180-mer) (55 kDa, DNA from Homo sapiens)
- The p300 catalytic core bound to the h4k12ack16ac nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)