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 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]
- Palmitic acid (256 Da, Ligand)
- Cholesterol (386 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)
- Human svct1 dimer in an apo inward-open state (Complex from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, 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 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]
- Palmitic acid (256 Da, Ligand)
- Ascorbic acid (176 Da, Ligand)
- Water (18 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Human svct1 dimer in a substrate-bound inward-open state (Complex from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Sodium ion (22 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 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]
- Palmitic acid (256 Da, Ligand)
- Water (18 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Solute carrier family 23 member 1 (64 kDa, Protein from Homo sapiens)
- Human svct1 dimer in an apo occluded state (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
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 ]
- Prestin (82 kDa, Protein from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- 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)
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 ]
- Prestin (82 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Prestin in complex with chloride ion (Complex from Homo sapiens)
- 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 [ Pubmed: 36266333 DOI: doi:10.1038/s41467-022-34017-x ]
- 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)
- 2-hydroxybenzoic acid (138 Da, Ligand)
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 ]
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- (2s)-2-azanyl-4-[[4-[2-bromanyl-4,5-bis(fluoranyl)phenoxy]phenyl]amino]-4-oxidanylidene-butanoic acid (415 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Eaat2 (Complex from Homo sapiens)
- Excitatory amino acid transporter 2 (63 kDa, Protein from Homo sapiens)
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
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 ]
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Eaat2 (Complex from Homo sapiens)
- Excitatory amino acid transporter 2 (63 kDa, Protein from Homo sapiens)
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 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 [ Pubmed: 32832629 DOI: doi:10.1126/sciadv.aba8105 ]
- Calcium homeostasis modulator 1 (35 kDa, Protein from Oryzias latipes)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Calhm1 (Complex from Oryzias latipes)
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class1)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6k7g
Q-score: 0.494
Hiraizumi M, Yamashita K, Nishizawa T, Nureki O
Science (2019) 365 pp. 1149-1155 [ Pubmed: 31416931 DOI: doi:10.1126/science.aay3353 ]
- Cholesterol hemisuccinate (486 Da, Ligand)
- Atp8a1-cdc50a (Complex from Homo sapiens)
- Cell cycle control protein 50a (40 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Phospholipid-transporting atpase (130 kDa, Protein from Homo sapiens)