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RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease
Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, Nishimasu H
Science (2022) 378 pp. 882-889 [ DOI: 10.1126/science.add7347 Pubmed: 36423304 ]
Image sets:
Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex
Kato K, Zhou W, Okazaki S, Isayama Y, Nishizawa T, Gootenberg JS, Abudayyeh OO, Nishimasu H
Cell (2022) 185 pp. 2324-2337.e16 [ Pubmed: 35643083 DOI: 10.1016/j.cell.2022.05.003 ]
Image sets:
Cyo-EM structure of wildtype non-gastric proton pump in the presence of Na+, AlF and ADP
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 8ijl
Q-score: 0.612
Biochim Biophys Acta Mol Cell Res (2023) 1870 pp. 119543-119543 [ DOI: doi:10.1016/j.bbamcr.2023.119543 Pubmed: 37482134 ]
- Sodium/potassium-transporting atpase subunit alpha (109 kDa, Protein from Rattus)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Sodium/potassium-transporting atpase subunit beta-1 (37 kDa, Protein from Rattus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Hetero dimer of alpha and beta subunit (135 MDa, Complex from Rattus)
- Water (18 Da, Ligand)
- 2-{[(4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranoside (1 kDa, Ligand)
- Cholesterol (386 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium ion (22 Da, Ligand)
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 (Complex from Homo sapiens)
- Bre1 (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Bre1-nucleosome complex (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase bre1b (113 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase bre1a (113 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex)
- Histone h2a type 1 (13 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 ]
- Bre1-nucleosome complex (Complex from Homo sapiens)
- Hiistone (Complex)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
Cyo-EM structure of K794A non-gastric proton pump in Na+ bound E1AMPPCP state
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8ijm
Q-score: 0.412
Biochim Biophys Acta Mol Cell Res (2023) 1870 pp. 119543-119543 [ DOI: doi:10.1016/j.bbamcr.2023.119543 Pubmed: 37482134 ]
- Sodium/potassium-transporting atpase subunit alpha (109 kDa, Protein from Rattus)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Sodium/potassium-transporting atpase subunit beta-1 (37 kDa, Protein from Rattus)
- Hetero dimer of alpha and beta subunit (135 MDa, Complex from Rattus)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium ion (22 Da, Ligand)
Cryo-EM structure of non-gastric proton pump K794S mutant in Na+ bound E1AMPPCP state
Biochim Biophys Acta Mol Cell Res (2023) 1870 pp. 119543-119543 [ DOI: doi:10.1016/j.bbamcr.2023.119543 Pubmed: 37482134 ]
- Hetero dimer of alpha and beta subunit (135 MDa, Complex from Rattus)
Thermostabilized human prestin in complex with chloride, sulfate or salicylate
Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O
Nat Commun (2022) 13 [ Pubmed: 36266333 DOI: 10.1038/s41467-022-34017-x ]
Image sets:
Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer
Nagiri C, Kobayashi K, Tomita A, Kato M, Kobayashi K, Yamashita K, Nishizawa T, Inoue A, Shihoya W, Nureki O
Mol Cell (2021) 81 pp. 3205-321500000.0 [ DOI: 10.1016/j.molcel.2021.06.024 Pubmed: 34314699 ]
Image sets:
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 [ DOI: doi:10.1038/s41467-022-34378-3 Pubmed: 36344504 ]
- Iscb-omegarna (Complex from metagenome)
- Ogeuiscb (56 kDa, Protein from metagenome)
- Dna (5'-d(p*gp*ap*ap*gp*ap*ap*ap*ap*cp*cp*ap*t)-3') (4 kDa, DNA from synthetic construct)
- Structure of the iscb-omegarna ribonucleoprotein complex (Complex)
- Dna (49-mer) (15 kDa, DNA from synthetic construct)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Rna (228-mer) (73 kDa, RNA from metagenome)
- Magnesium ion (24 Da, Ligand)
- Dna (Complex)