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
- 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)
- 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 light chain (23 kDa, Protein from Mus musculus)
- Fab-b heavy chain (22 kDa, Protein from Mus musculus)
- Membrane protein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 M protein dimer (long form) in complex with Fab-E and incubated with CIM-834
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
To Be Published
- Fab-e light chain (Protein from Mus musculus)
- Fab-e heavy chain (Protein from Mus musculus)
- Membrane protein (Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 m protein dimer (long form) in complex with fab-e and incubated with cim-834 (154 kDa, Complex 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 ]
- High affinity immunoglobulin epsilon receptor subunit alpha (32 kDa, Protein from Homo sapiens)
- Ige fc (39 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Human fc epsilon ri in complex with hige fc (Complex from Homo sapiens)
Human Fc epsilon RI in complex with mIgE Fc (TMD disordered)
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8k7s
Q-score: 0.358
Zhang Z, Yui M, Ohto U, Shimizu T
Sci Signal (2024) 17 pp. eadn1303-eadn1303 [ DOI: doi:10.1126/scisignal.adn1303 Pubmed: 39656861 ]
- Fcer1a (32 kDa, Protein from Homo sapiens)
- Ige fc (40 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Human fc epsilon ri in complex with mige fc (Complex 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)
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 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Mouse fc epsilon ri in complex with mige fc (Complex from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit alpha (31 kDa, Protein from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit gamma (11 kDa, Protein from Mus musculus)
- Ige fc (40 kDa, Protein from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit beta (27 kDa, Protein from Mus musculus)
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 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- High affinity immunoglobulin epsilon receptor subunit gamma (11 kDa, Protein from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit alpha (31 kDa, Protein from Mus musculus)
- Mouse fc epsilon ri (Complex from Mus musculus)
- High affinity immunoglobulin epsilon receptor subunit beta (27 kDa, Protein from Mus musculus)
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 ]
- Sid1 transmembrane family member 1 (96 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Homo-dimer of sidt1 (Complex from Homo sapiens)
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 ]
- Sid1 transmembrane family member 1 (96 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Homodimer of sidt1 (Complex from Homo sapiens)
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)
- Fab heavy chain from antibody igg clone number yn9048 (26 kDa, Protein from Ondatra zibethicus)
- Pres1 protein (fragment) (6 kDa, Protein from Hepatitis B virus)
- Fab light chain from antibody igg clone number yn9048 (23 kDa, Protein from Ondatra zibethicus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)