Human sodium-dependent vitamin C transporter 1 in an apo inward-open state
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8jez
Q-score: 0.616
Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O
Nat Commun (2024) 15 pp. 5569-5569 [ DOI: doi:10.1038/s41467-024-49899-2 Pubmed: 38956111 ]
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Human svct1 dimer in an apo inward-open state (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
Human sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state
Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O
Nat Commun (2024) 15 pp. 5569-5569 [ DOI: doi:10.1038/s41467-024-49899-2 Pubmed: 38956111 ]
- Water (18 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Human svct1 dimer in a substrate-bound inward-open state (Complex from Homo sapiens)
- Ascorbic acid (176 Da, Ligand)
Human sodium-dependent vitamin C transporter 1 in an apo occluded state
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8jf1
Q-score: 0.595
Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O
Nat Commun (2024) 15 pp. 5569-5569 [ DOI: doi:10.1038/s41467-024-49899-2 Pubmed: 38956111 ]
- Water (18 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Human svct1 dimer in an apo occluded state (Complex from Homo sapiens)
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 [ Pubmed: 36266333 DOI: doi:10.1038/s41467-022-34017-x ]
- Chloride ion (35 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- Prestin (82 kDa, Protein from Homo sapiens)
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 [ Pubmed: 36266333 DOI: doi:10.1038/s41467-022-34017-x ]
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Sulfate ion (96 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Prestin (82 kDa, Protein from Homo sapiens)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
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 [ Pubmed: 36266333 DOI: doi:10.1038/s41467-022-34017-x ]
- 2-hydroxybenzoic acid (138 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Prestin (82 kDa, Protein from Homo sapiens)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
Inward-facing structure of human EAAT2 in the WAY213613-bound state
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 7vr7
Q-score: 0.553
Kato T, Kusakizako T, Jin C, Zhou X, Ohgaki R, Quan L, Xu M, Okuda S, Kobayashi K, Yamashita K, Nishizawa T, Kanai Y, Nureki O
Nat Commun (2022) 13 pp. 4714-4714 [ Pubmed: 35953475 DOI: doi:10.1038/s41467-022-32442-6 ]
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- (2s)-2-azanyl-4-[[4-[2-bromanyl-4,5-bis(fluoranyl)phenoxy]phenyl]amino]-4-oxidanylidene-butanoic acid (415 Da, Ligand)
- Eaat2 (Complex from Homo sapiens)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Excitatory amino acid transporter 2 (63 kDa, Protein from Homo sapiens)
Inward-facing structure of human EAAT2 in the substrate-free state
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 7vr8
Q-score: 0.431
Kato T, Kusakizako T, Jin C, Zhou X, Ohgaki R, Quan L, Xu M, Okuda S, Kobayashi K, Yamashita K, Nishizawa T, Kanai Y, Nureki O
Nat Commun (2022) 13 pp. 4714-4714 [ Pubmed: 35953475 DOI: doi:10.1038/s41467-022-32442-6 ]
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- Eaat2 (Complex from Homo sapiens)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Excitatory amino acid transporter 2 (63 kDa, Protein from Homo sapiens)
2.02 angstrom cryo-EM structure of the pump-like channelrhodopsin ChRmine
Resolution: 2.02 Å
EM Method: Single-particle
Fitted PDBs: 7w9w
Q-score: 0.708
Kishi KE, Kim YS, Fukuda M, Inoue M, Kusakizako T, Wang PY, Ramakrishnan C, Byrne EFX, Thadhani E, Paggi JM, Matsui TE, Yamashita K, Nagata T, Konno M, Quirin S, Lo M, Benster T, Uemura T, Liu K, Shibata M, Nomura N, Iwata S, Nureki O, Dror RO, Inoue K, Deisseroth K, Kato HE
Cell (2022) 185 pp. 672- [ DOI: doi:10.1016/j.cell.2022.01.007 Pubmed: 35114111 ]
- Water (18 Da, Ligand)
- Chrmine (Complex from Rhodomonas lens)
- Retinal (284 Da, Ligand)
- Chrmine (35 kDa, Protein from Rhodomonas lens)
- Cholesterol (386 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
Cryo-EM structure of the killifish CALHM1
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 6lmt
Q-score: 0.561
Demura K, Kusakizako T, Shihoya W, Hiraizumi M, Nomura K, Shimada H, Yamashita K, Nishizawa T, Taruno A, Nureki O
Sci Adv (2020) 6 pp. eaba8105-eaba8105 [ DOI: doi:10.1126/sciadv.aba8105 Pubmed: 32832629 ]
- Calhm1 (Complex from Oryzias latipes)
- Calcium homeostasis modulator 1 (35 kDa, Protein from Oryzias latipes)
- Cholesterol hemisuccinate (486 Da, Ligand)