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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)
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)
Thermostabilized human prestin in complex with chloride
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 7v73
Q-score: 0.488
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 pp. 6208-6208 [ DOI: doi:10.1038/s41467-022-34017-x Pubmed: 36266333 ]
- Cholesterol (386 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- Prestin (82 kDa, Protein from Homo sapiens)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
Thermostabilized human prestin in complex with sulfate
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 7v74
Q-score: 0.5
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 pp. 6208-6208 [ DOI: doi:10.1038/s41467-022-34017-x Pubmed: 36266333 ]
- Prestin (82 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Sulfate ion (96 Da, Ligand)
Thermostabilized human prestin in complex with salicylate
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 7v75
Q-score: 0.488
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 pp. 6208-6208 [ DOI: doi:10.1038/s41467-022-34017-x Pubmed: 36266333 ]
- Prestin (82 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- 2-hydroxybenzoic acid (138 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
human NTCP in complex with YN69083 Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7fci
Q-score: 0.497
Park JH, Iwamoto M, Yun JH, Uchikubo-Kamo T, Son D, Jin Z, Yoshida H, Ohki M, Ishimoto N, Mizutani K, Oshima M, Muramatsu M, Wakita T, Shirouzu M, Liu K, Uemura T, Nomura N, Iwata S, Watashi K, Tame JRH, Nishizawa T, Lee W, Park SY
Nature (2022) 606 pp. 1027-1031 [ Pubmed: 35580630 DOI: doi:10.1038/s41586-022-04857-0 ]
- Fab heavy chain (27 kDa, Protein from Mus musculus)
- Human ntcp in complex with yn69083 (89 kDa, Cellular component)
- Fab light chain,fab heavy chain (Complex from Mus musculus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab light chain (23 kDa, Protein from Mus musculus)
- Ntcp (Complex from Homo sapiens)