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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 ]
- Cholesterol (386 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Sodium/potassium-transporting atpase subunit beta-1 (37 kDa, Protein from Rattus)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Water (18 Da, Ligand)
- Hetero dimer of alpha and beta subunit (135 MDa, Complex from Rattus)
- Sodium ion (22 Da, Ligand)
- Sodium/potassium-transporting atpase subunit alpha (109 kDa, Protein from Rattus)
- Magnesium ion (24 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)
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)
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 ]
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Sodium/potassium-transporting atpase subunit beta-1 (37 kDa, Protein from Rattus)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hetero dimer of alpha and beta subunit (135 MDa, Complex from Rattus)
- Sodium ion (22 Da, Ligand)
- Sodium/potassium-transporting atpase subunit alpha (109 kDa, Protein from Rattus)
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)
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)
Structure of the Cas7-11-Csx29-guide RNA complex
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 7y9x
Q-score: 0.59
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: doi:10.1126/science.add7347 Pubmed: 36423304 ]
- Cas7-11, csx29 (Complex from Desulfonema ishimotonii)
- Crrna (12 kDa, RNA from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Rna (Complex)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Zinc ion (65 Da, Ligand)
Structure of the Cas7-11-Csx29-guide RNA-target RNA (no PFS) complex
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 7y9y
Q-score: 0.564
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: doi:10.1126/science.add7347 Pubmed: 36423304 ]
- Rna (38-mer) (12 kDa, RNA from Desulfonema ishimotonii)
- Cas7-11, csx29 (Complex)
- Rna (27-mer) (8 kDa, RNA from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Crrna, target rna (Complex from Desulfonema ishimotonii)
- Zinc ion (65 Da, Ligand)
Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8gs2
Q-score: 0.571
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: doi:10.1126/science.add7347 Pubmed: 36423304 ]
- Crrna (30 kDa, RNA from Desulfonema ishimotonii)
- Cas7-11, csx29 (Complex)
- Adenosine monophosphate (347 Da, Ligand)
- Cytidine-5'-monophosphate (323 Da, Ligand)
- Target rna with non-matching pfs (10 kDa, RNA from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Crrna (Complex)
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Target rna with 3'-tag (Complex from Desulfonema ishimotonii)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of non gastric H,K-ATPase alpha2 K794A in (K+)E2-AlF state
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7x21
Q-score: 0.566
Young VC, Nakanishi H, Meyer DJ, Nishizawa T, Oshima A, Artigas P, Abe K
Nat Commun (2022) 13 pp. 5270-5270 [ Pubmed: 36085139 DOI: doi:10.1038/s41467-022-32793-0 ]
- Cholesterol (386 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase alpha chain 2 (109 kDa, Protein from Rattus norvegicus)
- Sodium/potassium-transporting atpase subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Non gastric h,k-atpase (150 MDa, Complex from Rattus norvegicus)