mouse TMEM63b in LMNG-CHS micelle
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8wg3
Q-score: 0.456
Miyata Y, Takahashi K, Lee Y, Sultan CS, Kuribayashi R, Takahashi M, Hata K, Bamba T, Izumi Y, Liu K, Uemura T, Nomura N, Iwata S, Nagata S, Nishizawa T, Segawa K
To Be Published
- Mouse tmem63b (100 kDa, Complex from Mus musculus)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Csc1-like protein 2,green fluorescent protein (126 kDa, Protein from Aequorea victoria)
- Cholesterol hemisuccinate (486 Da, Ligand)
mouse TMEM63b in DDM-CHS micelle with YN9303-24 Fab
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8wg4
Q-score: 0.478
Miyata Y, Takahashi K, Lee Y, Sultan CS, Kuribayashi R, Takahashi M, Hata K, Bamba T, Izumi Y, Liu K, Uemura T, Nomura N, Iwata S, Nagata S, Nishizawa T, Segawa K
To Be Published
- Mouse tmem63b (100 kDa, Complex from Mus musculus)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Csc1-like protein 2,green fluorescent protein (126 kDa, Protein from Aequorea victoria)
- Cholesterol hemisuccinate (486 Da, Ligand)
Cryo-EM structure of human XKR8-basigin complex in lipid nanodisc
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8xej
Q-score: 0.415
Sakuragi T, Kanai R, Otani M, Kikkawa M, Toyoshima C, Nagata S
J Biol Chem (2024) 300 pp. 105755-105755 [ Pubmed: 38364890 DOI: doi:10.1016/j.jbc.2024.105755 ]
- Human xkr8-basigin complex bound to fab fragment in lipid nanodisc (110 kDa, Complex)
- Fab heavy chain (22 kDa, Protein from Oryctolagus cuniculus)
- Human xkr8-basigin complex (Complex from Homo sapiens)
- 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (782 Da, Ligand)
- Xk-related protein 8 (45 kDa, Protein from Homo sapiens)
- Isoform 2 of basigin (19 kDa, Protein from Homo sapiens)
- Fab fragment (Complex from Oryctolagus cuniculus)
- Fab light chain (23 kDa, Protein from Oryctolagus cuniculus)
Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 8hlb
Q-score: 0.446
Akiba H, Fujita J, Ise T, Nishiyama K, Miyata T, Kato T, Namba K, Ohno H, Kamada H, Nagata S, Tsumoto K
Commun Biol (2023) 6 pp. 987-987 [ DOI: doi:10.1038/s42003-023-05326-8 Pubmed: 37758868 ]
- Tumor necrosis factor receptor superfamily member 1b,maltose/maltodextrin-binding periplasmic protein (60 kDa, Protein from Escherichia coli (strain K12))
- Tr109 heavy chain (25 kDa, Protein from Homo sapiens)
- Tr109 light chain (23 kDa, Protein from Homo sapiens)
- Cryo-em structure of biparatopic antibody bp109-92 in complex with tnfr2 (Complex from Homo sapiens)
- Tr92 light chain (23 kDa, Protein from Homo sapiens)
- Tr92 heavy chain (25 kDa, Protein from Homo sapiens)
Human Xkr8-Basigin complex bound to Fab fragment
Sakuragi T, Kanai R, Tsutsumi A, Narita H, Onishi E, Nishino K, Miyazaki T, Baba T, Kosako H, Nakagawa A, Kikkawa M, Toyoshima C, Nagata S
Nat Struct Mol Biol (2021) 28 pp. 825-834 [ DOI: 10.1038/s41594-021-00665-8 Pubmed: 34625749 ]
Image sets:
Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7dce
Q-score: 0.423
Sakuragi T, Kanai R, Tsutsumi A, Narita H, Onishi E, Nishino K, Miyazaki T, Baba T, Kosako H, Nakagawa A, Kikkawa M, Toyoshima C, Nagata S
Nat Struct Mol Biol (2021) 28 pp. 825-834 [ Pubmed: 34625749 DOI: doi:10.1038/s41594-021-00665-8 ]
- Human xkr8-basigin complex (Complex from Homo sapiens)
- Light chain of fab fragment (23 kDa, Protein from Oryctolagus cuniculus)
- 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (782 Da, Ligand)
- Human xkr8-basigin complex bound to fab fragment (110 kDa, Complex)
- Heavy chain of fab fragment (22 kDa, Protein from Oryctolagus cuniculus)
- Xk-related protein 8 (45 kDa, Protein from Homo sapiens)
- Isoform 2 of basigin (19 kDa, Protein from Homo sapiens)
- Fab fragment (Complex from Oryctolagus cuniculus)
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1-AMPPCP state
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7bsp
Q-score: 0.477
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ DOI: doi:10.1016/j.celrep.2020.108208 Pubmed: 32997992 ]
- Atp11c (124 kDa, Protein from Homo sapiens)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF-ADP state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7bsq
Q-score: 0.567
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ DOI: doi:10.1016/j.celrep.2020.108208 Pubmed: 32997992 ]
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp11c (124 kDa, Protein from Homo sapiens)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7bss
Q-score: 0.539
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ DOI: doi:10.1016/j.celrep.2020.108208 Pubmed: 32997992 ]
- Alpha-d-mannopyranose (180 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp11c (124 kDa, Protein from Homo sapiens)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-bound E2BeF state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7bsu
Q-score: 0.572
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ DOI: doi:10.1016/j.celrep.2020.108208 Pubmed: 32997992 ]
- Atp11c (124 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Cell cycle control protein 50a (40 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- 1-deoxy-alpha-d-mannopyranose (164 Da, Ligand)