Resolution: 3.55 Å
EM Method: Single-particle
Fitted PDBs: 9j7i
Q-score: 0.482
Yamaguchi H, Kitajima S, Suzuki H, Suzuki S, Nishikawa K, Kamegawa A, Fujiyoshi Y, Takahashi K, Tagami U, Maruyama Y, Kuroda M, Sugiki M
Sci Rep (2025) 15 pp. 3894-3894 [ DOI: doi:10.1038/s41598-025-87999-1 Pubmed: 39890873 ]
- Gamma-glutamyl-valyl-glycine (303 Da, Protein from synthetic construct)
- Extracellular regions of calcium-sensing receptor (Complex from Homo sapiens)
- Extracellular calcium-sensing receptor (101 kDa, Protein from Homo sapiens)
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 8ydx
Q-score: 0.237
Nakamura S, Tanimura Y, Nomura R, Suzuki H, Nishikawa K, Kamegawa A, Numoto N, Tanaka A, Kawabata S, Sakaguchi S, Emi A, Suzuki Y, Fujiyoshi Y
To Be Published
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cespiace (4 kDa, Protein from synthetic construct)
- Sars-cov-2 spike ectodomain (hexapro, omicron ba.2 variant) in complex with cespiace (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 8ydy
Q-score: 0.084
Nakamura S, Tanimura Y, Nomura R, Suzuki H, Nishikawa K, Kamegawa A, Numoto N, Tanaka A, Kawabata S, Sakaguchi S, Emi A, Suzuki Y, Fujiyoshi Y
To Be Published
- Sars-cov-2 spike ectodomain (hexapro, omicron ba.5 variant) in complex with cespiace (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cespiace (4 kDa, Protein from synthetic construct)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 5.2 Å
EM Method: Single-particle
Fitted PDBs: 8ydz
Q-score: 0.2
Nakamura S, Tanimura Y, Nomura R, Suzuki H, Nishikawa K, Kamegawa A, Numoto N, Tanaka A, Kawabata S, Sakaguchi S, Emi A, Suzuki Y, Fujiyoshi Y
To Be Published
- Sars-cov-2 spike ectodomain (hexapro, omicron ba.5 variant) in complex with cespiace (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cespiace (4 kDa, Protein from synthetic construct)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of LPA1-Gi complex with LPA
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 9izf
Q-score: 0.487
Suzuki S, Tanaka K, Kamegawa A, Nishikawa K, Suzuki H, Oshima A, Fujiyoshi Y
J Struct Biol (2024) 217 pp. 108164-108164 [ DOI: doi:10.1016/j.jsb.2024.108164 Pubmed: 39725093 ]
- Soluble cytochrome b562,lysophosphatidic acid receptor 1,lgbit tag (73 kDa, Protein from synthetic construct)
- Scfv16 (26 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (41 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl (9e)-octadec-9-enoate (436 Da, Ligand)
- Multiprotein complex (Complex from Homo sapiens)
Cryo-EM structure of LPA1-Gq complex with LPA
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 9izg
Q-score: 0.557
Suzuki S, Tanaka K, Kamegawa A, Nishikawa K, Suzuki H, Oshima A, Fujiyoshi Y
J Struct Biol (2024) 217 pp. 108164-108164 [ DOI: doi:10.1016/j.jsb.2024.108164 Pubmed: 39725093 ]
- Soluble cytochrome b562,lysophosphatidic acid receptor 1,lgbit tag (73 kDa, Protein from synthetic construct)
- Scfv16 (26 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (41 kDa, Protein from Homo sapiens)
- Gs-mini-gq chimera (28 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl (9e)-octadec-9-enoate (436 Da, Ligand)
- Multiprotein complex (Complex from Homo sapiens)
Cryo-EM structure of LPA1-G13 complex with LPA
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 9izh
Q-score: 0.553
Suzuki S, Tanaka K, Kamegawa A, Nishikawa K, Suzuki H, Oshima A, Fujiyoshi Y
J Struct Biol (2024) 217 pp. 108164-108164 [ DOI: doi:10.1016/j.jsb.2024.108164 Pubmed: 39725093 ]
- Soluble cytochrome b562,lysophosphatidic acid receptor 1,lgbit tag (73 kDa, Protein from synthetic construct)
- G protein subunit 13 (gi2-mini-g13 chimera) (26 kDa, Protein from Homo sapiens)
- Scfv16 (26 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (41 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl (9e)-octadec-9-enoate (436 Da, Ligand)
- Multiprotein complex (Complex from Homo sapiens)
Structure of arginine oxidase from Pseudomonas sp. TRU 7192
Resolution: 2.34 Å
EM Method: Single-particle
Fitted PDBs: 8jt7
Q-score: 0.689
Yamaguchi H, Takahashi K, Numoto N, Suzuki H, Tatsumi M, Kamegawa A, Nishikawa K, Asano Y, Mizukoshi T, Miyano H, Fujiyoshi Y, Sugiki M
J.Biochem. (2025) 177 pp. 27-36 [ Pubmed: 39420599 DOI: doi:10.1093/jb/mvae070 ]
- Homooctamer of arginine oxidase (540 kDa, Complex from Pseudomonas sp.)
- Water (18 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Amine oxidoreductase (67 kDa, Protein from Pseudomonas sp.)
Single-particle Cryo-EM datasets of hydroxycarboxylic acid receptor signaling complexes
Suzuki S, Tanaka K, Nishikawa K, Suzuki H, Oshima A, Fujiyoshi Y
Nat Commun (2023) 14 [ DOI: 10.1038/s41467-023-41650-7 Pubmed: 37736747 ]
Image sets:
- Unaligned multi-frame TIFF compressed movies of the HCA2-Gi complex with GSK256073
- Unaligned multi-frame TIFF compressed movies of the HCA2-Gi complex with LUF6283
- Unaligned multi-frame TIFF compressed movies of the HCA2-Gi complex with acifran
- Unaligned multi-frame TIFF compressed movies of the HCA2-Gi complex with MK6892
- Unaligned multi-frame TIFF compressed movies of the HCA3-Gi complex with acifran
Cryo-EM structure of HCA2-Gi complex with GSK256073
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8ihb
Q-score: 0.571
Suzuki S, Tanaka K, Nishikawa K, Suzuki H, Oshima A, Fujiyoshi Y
Nat Commun (2023) 14 pp. 5899-5899 [ DOI: doi:10.1038/s41467-023-41650-7 Pubmed: 37736747 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (41 kDa, Protein from Mus musculus)
- 8-chloranyl-3-pentyl-7h-purine-2,6-dione (256 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- Scfv16 (26 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Multiprotein complex (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Soluble cytochrome b562,hydroxycarboxylic acid receptor 2 (74 kDa, Protein from Homo sapiens)