SARS-CoV-2 M protein dimer (short form) in complex with Fab-B and CIM-834
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9exa
Q-score: 0.503
Laporte M, Jochmans D, Bardiot D, Desmarets L, Debski-Antoniak OJ, Mizzon G, Abdelnabi R, Leyssen P, Chiu W, Zhang Z, Nomura N, Bolland S, Ohto U, Stahl Y, Wuyts J, De Jonghe S, Dubuisson J, Bosch BJ, van Kuppeveld JM, Eydoux C, Decroly E, Canard B, Naesens L, Snijder E, Belouzard S, Shimizu T, Bartenschlager R, Hurdiss DL, Marchand A, Chaltin P, Neyts J
To Be Published
- Sars-cov-2 m protein dimer (short form) in complex with fab-b and cim-834 (154 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab-b heavy chain (22 kDa, Protein from Mus musculus)
- 6-[[1-[4,6-dimethyl-5-(2-methylpropyl)pyrimidin-2-yl]piperidin-4-yl]-methyl-amino]-n-(2-pyrrolidin-1-ylethyl)pyridazine-4-carboxamide (494 Da, Ligand)
- Fab-b light chain (23 kDa, Protein from Mus musculus)
- Membrane protein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Human Fc epsilon RI in complex with hIgE Fc (TMD disordered)
Resolution: 3.56 Å
EM Method: Single-particle
Fitted PDBs: 8k7r
Q-score: 0.452
Zhang Z, Yui M, Ohto U, Shimizu T
Sci Signal (2024) 17 pp. eadn1303-eadn1303 [ DOI: doi:10.1126/scisignal.adn1303 Pubmed: 39656861 ]
- Ige fc (39 kDa, Protein from Homo sapiens)
- Human fc epsilon ri in complex with hige fc (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- High affinity immunoglobulin epsilon receptor subunit alpha (32 kDa, Protein from Homo sapiens)
Cryo-EM structure of mouse SLC15A3 (outward-facing open)
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 8wx1
Q-score: 0.384
Zhang Z, Kasai S, Sakaniwa K, Fujimura A, Ohto U, Shimizu T
To Be Published
- Mouse slc15a3 (Complex)
- Mouse slc15a3 (Complex from Mus musculus)
- Solute carrier family 15 member 3 (64 kDa, Protein from Mus musculus)
Cryo-EM structure of TLR7/TH-407b complex
To Be Published
- (1s,3r)-5-[4-(8-nitroquinolin-5-yl)piperazin-1-yl]carbonyladamantan-2-one (434 Da, Ligand)
- Toll-like receptor 7 (94 kDa, Protein from Macaca mulatta)
- Tlr7 (Complex from Macaca mulatta)
Mouse Fc epsilon RI in complex with mIgE Fc
Resolution: 3.71 Å
EM Method: Single-particle
Fitted PDBs: 8k7t
Q-score: 0.37
Zhang Z, Yui M, Ohto U, Shimizu T
Sci Signal (2024) 17 pp. eadn1303-eadn1303 [ DOI: doi:10.1126/scisignal.adn1303 Pubmed: 39656861 ]
- High affinity immunoglobulin epsilon receptor subunit alpha (31 kDa, Protein from Mus musculus)
- Mouse fc epsilon ri in complex with mige fc (Complex from Mus musculus)
- Ige fc (40 kDa, Protein from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit beta (27 kDa, Protein from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit gamma (11 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.87 Å
EM Method: Single-particle
Fitted PDBs: 8yrj
Q-score: 0.271
Zhang Z, Yui M, Ohto U, Shimizu T
Sci Signal (2024) 17 pp. eadn1303-eadn1303 [ DOI: doi:10.1126/scisignal.adn1303 Pubmed: 39656861 ]
- High affinity immunoglobulin epsilon receptor subunit alpha (31 kDa, Protein from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit beta (27 kDa, Protein from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit gamma (11 kDa, Protein from Mus musculus)
- Mouse fc epsilon ri (Complex from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of human SIDT1 bound to cholesterol
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8kcw
Q-score: 0.542
Hirano Y, Ohto U, Ichi I, Sato R, Miyake K, Shimizu T
Commun Biol (2024) 7 pp. 664-664 [ DOI: doi:10.1038/s42003-024-06346-8 Pubmed: 38811802 ]
- Cholesterol (386 Da, Ligand)
- Homo-dimer of sidt1 (Complex from Homo sapiens)
- Sid1 transmembrane family member 1 (96 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of human SIDT1
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8kcx
Q-score: 0.502
Hirano Y, Ohto U, Ichi I, Sato R, Miyake K, Shimizu T
Commun Biol (2024) 7 pp. 664-664 [ DOI: doi:10.1038/s42003-024-06346-8 Pubmed: 38811802 ]
- Homodimer of sidt1 (Complex from Homo sapiens)
- Sid1 transmembrane family member 1 (96 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8hrx
Q-score: 0.523
Asami J, Park JH, Nomura Y, Kobayashi C, Mifune J, Ishimoto N, Uemura T, Liu K, Sato Y, Zhang Z, Muramatsu M, Wakita T, Drew D, Iwata S, Shimizu T, Watashi K, Park SY, Nomura N, Ohto U
Nat Struct Mol Biol (2024) 31 pp. 447-454 [ Pubmed: 38233573 DOI: doi:10.1038/s41594-023-01191-5 ]
- Ntcp-myr-pres1-yn9048fab (Complex from Homo sapiens)
- Pres1 protein (fragment) (6 kDa, Protein from Hepatitis B virus)
- Fab heavy chain from antibody igg clone number yn9048 (26 kDa, Protein from Ondatra zibethicus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab light chain from antibody igg clone number yn9048 (23 kDa, Protein from Ondatra zibethicus)
Cryo-EM structure of human NTCP-myr-preS1-YN9016Fab complex
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 8hry
Q-score: 0.523
Asami J, Park JH, Nomura Y, Kobayashi C, Mifune J, Ishimoto N, Uemura T, Liu K, Sato Y, Zhang Z, Muramatsu M, Wakita T, Drew D, Iwata S, Shimizu T, Watashi K, Park SY, Nomura N, Ohto U
Nat Struct Mol Biol (2024) 31 pp. 447-454 [ Pubmed: 38233573 DOI: doi:10.1038/s41594-023-01191-5 ]
- Fab light chain from antibody igg clone number yn9016 (23 kDa, Protein from Ondatra zibethicus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab heavy chain from antibody igg clone number yn9016 (25 kDa, Protein from Ondatra zibethicus)
- Large s protein (fragment) (6 kDa, Protein from Hepatitis B virus)
- Ntcp-myr-pres1-yn9016fab (Complex from Homo sapiens)