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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 h4 (11 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase bre1b (113 kDa, Protein from Homo sapiens)
- Histone (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase bre1a (113 kDa, Protein from Homo sapiens)
- Bre1 (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 (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Bre1-nucleosome complex (Complex)
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 h4 (11 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Bre1-nucleosome complex (Complex from Homo sapiens)
- Dna (147-mer) (45 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)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Hiistone (Complex)
Structure of the OgeuIscB-omega RNA-target DNA complex
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 7xht
Q-score: 0.619
Kato K, Okazaki S, Kannan S, Altae-Tran H, Esra Demircioglu F, Isayama Y, Ishikawa J, Fukuda M, Macrae RK, Nishizawa T, Makarova KS, Koonin EV, Zhang F, Nishimasu H
Nat Commun (2022) 13 pp. 6719-6719 [ Pubmed: 36344504 DOI: doi:10.1038/s41467-022-34378-3 ]
- Dna (Complex)
- Dna (5'-d(p*gp*ap*ap*gp*ap*ap*ap*ap*cp*cp*ap*t)-3') (4 kDa, DNA from synthetic construct)
- Rna (228-mer) (73 kDa, RNA from metagenome)
- Iscb-omegarna (Complex from metagenome)
- Dna (49-mer) (15 kDa, DNA from synthetic construct)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Structure of the iscb-omegarna ribonucleoprotein complex (Complex)
- Ogeuiscb (56 kDa, Protein from metagenome)
Cryo-EM structure of the Cas13bt3-crRNA-target RNA ternary complex
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7vtn
Q-score: 0.3
Nakagawa R, Kannan S, Altae-Tran H, Takeda SN, Tomita A, Hirano H, Kusakizako T, Nishizawa T, Yamashita K, Zhang F, Nishimasu H, Nureki O
Mol Cell (2022) 82 pp. 3178-3192.e5 [ Pubmed: 36027912 DOI: doi:10.1016/j.molcel.2022.08.001 ]
- Cas13bt3-crrna-target rna (Complex)
- Cas13bt3 (90 kDa, Protein from Planctomycetes bacterium)
- Crrna-target rna (Complex from Planctomycetes bacterium)
- Target rna (7 kDa, RNA from synthetic construct)
- Cas13bt3 (Complex)
- Crrna (19 kDa, RNA from synthetic construct)
Cryo-EM structure of the Cas12c2-sgRNA-target DNA ternary complex
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7v94
Q-score: 0.561
Kurihara N, Nakagawa R, Hirano H, Okazaki S, Tomita A, Kobayashi K, Kusakizako T, Nishizawa T, Yamashita K, Scott DA, Nishimasu H, Nureki O
Mol Cell (2022) 82 pp. 1865-1877.e4 [ Pubmed: 35366394 DOI: doi:10.1016/j.molcel.2022.03.006 ]
- Dna (Complex)
- Target dna (non target strand) (10 kDa, DNA from synthetic construct)
- Cas12c2-sgrna-dna complex (Complex from uncultured archaeon)
- Target dna (target strand) (10 kDa, DNA from synthetic construct)
- Sgrna (Complex)
- Cas12c2 (138 kDa, Protein from uncultured archaeon)
- Cas12c2 (Complex from uncultured archaeon)
- Sgrna (36 kDa, RNA from uncultured archaeon)
NSD2 E1099K mutant bound to nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7e8d
Q-score: 0.556
Sato K, Kumar A, Hamada K, Okada C, Oguni A, Machiyama A, Sakuraba S, Nishizawa T, Nureki O, Kono H, Ogata K, Sengoku T
Nat Commun (2021) 12 pp. 6605-6605 [ Pubmed: 34782608 DOI: doi:10.1038/s41467-021-26913-5 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nsd2-nucleosome complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone-lysine n-methyltransferase nsd2 (28 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (185-mer) (56 kDa, DNA from synthetic construct)
- Sinefungin (381 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (185-mer) (57 kDa, DNA from synthetic construct)
Cryo-EM structure of the Cas12f1-sgRNA-target DNA complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7c7l
Q-score: 0.516
Takeda SN, Nakagawa R, Okazaki S, Hirano H, Kobayashi K, Kusakizako T, Nishizawa T, Yamashita K, Nishimasu H, Nureki O
Mol Cell (2021) 81 pp. 558-570.e3 [ Pubmed: 33333018 DOI: doi:10.1016/j.molcel.2020.11.035 ]
- Cryo-em structure of the cas12f1-sgrna-target dna complex (Complex from uncultured archaeon)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Sgrna (Cellular component)
- Crispr-associated protein cas14a.1 (62 kDa, Protein from uncultured archaeon)
- Sgrna (58 kDa, RNA from uncultured archaeon)
- Target dna (Complex)
- Zinc ion (65 Da, Ligand)
- Cas12f1 (Complex)