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)
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)
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 ]
- Large s protein (fragment) (6 kDa, Protein from Hepatitis B virus)
- Fab light chain from antibody igg clone number yn9016 (23 kDa, Protein from Ondatra zibethicus)
- Fab heavy chain from antibody igg clone number yn9016 (25 kDa, Protein from Ondatra zibethicus)
- Ntcp-myr-pres1-yn9016fab (Complex from Homo sapiens)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7vgr
Q-score: 0.504
Zhang Z, Nomura N, Muramoto Y, Ekimoto T, Uemura T, Liu K, Yui M, Kono N, Aoki J, Ikeguchi M, Noda T, Iwata S, Ohto U, Shimizu T
Nat Commun (2022) 13 pp. 4399-4399 [ Pubmed: 35931673 DOI: doi:10.1038/s41467-022-32019-3 ]
- Membrane protein (28 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yn7756_1 fab (Complex from Mus musculus)
- Sars-cov-2 m protein dimer (long form) in complex with yn7756_1 fab (Complex)
- Yn7756_1 fab heavy chain (25 kDa, Protein from Mus musculus)
- Yn7756_1 fab light chain (24 kDa, Protein from Mus musculus)
- Membrane protein (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7vgs
Q-score: 0.451
Zhang Z, Nomura N, Muramoto Y, Ekimoto T, Uemura T, Liu K, Yui M, Kono N, Aoki J, Ikeguchi M, Noda T, Iwata S, Ohto U, Shimizu T
Nat Commun (2022) 13 pp. 4399-4399 [ Pubmed: 35931673 DOI: doi:10.1038/s41467-022-32019-3 ]
- Membrane protein (28 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yn7717_9 fab heavy chain (24 kDa, Protein from Mus musculus)
- Yn7717_9 fab (Complex from Mus musculus)
- Sars-cov-2 m protein dimer (short form) in complex with yn7717_9 fab (Complex)
- Membrane protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Yn7717_9 fab light chain (23 kDa, Protein from Mus musculus)
Cryo-EM structure of human NTCP complexed with YN69202Fab
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 7vad
Q-score: 0.399
Asami J, Kimura KT, Fujita-Fujiharu Y, Ishida H, Zhang Z, Nomura Y, Liu K, Uemura T, Sato Y, Ono M, Yamamoto M, Noda T, Shigematsu H, Drew D, Iwata S, Shimizu T, Nomura N, Ohto U
Nature (2022) 606 pp. 1021-1026 [ DOI: doi:10.1038/s41586-022-04845-4 Pubmed: 35580629 ]
- Fab light chain from antibody igg clone number yn69202 (24 kDa, Protein from Mus musculus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab (Complex)
- Complex of ntcp and fab (Complex from Homo sapiens)
- Fab heavy chain from antibody igg clone number yn69202 (26 kDa, Protein from Mus musculus)
- Ntcp: (Complex from Mus musculus)
Cryo-EM structure of bovine NTCP complexed with YN69202Fab
Resolution: 3.55 Å
EM Method: Single-particle
Fitted PDBs: 7vae
Q-score: 0.4
Asami J, Kimura KT, Fujita-Fujiharu Y, Ishida H, Zhang Z, Nomura Y, Liu K, Uemura T, Sato Y, Ono M, Yamamoto M, Noda T, Shigematsu H, Drew D, Iwata S, Shimizu T, Nomura N, Ohto U
Nature (2022) 606 pp. 1021-1026 [ DOI: doi:10.1038/s41586-022-04845-4 Pubmed: 35580629 ]
- Ntcp (Complex from Mus musculus)
- Fab light chain from antibody igg clone number yn69202 (24 kDa, Protein from Mus musculus)
- Fab heavy chain from antibody igg clone number yn69202 (26 kDa, Protein from Mus musculus)
- Solute carrier family 10 (sodium/bile acid cotransporter family), member 1 (38 kDa, Protein from Bos taurus)
- Fab (Complex)
- Complex of ntcp and fab (Complex from Homo sapiens)
Cryo-EM structure of Rat NTCP complexed with YN69202Fab
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 7vaf
Q-score: 0.461
Asami J, Kimura KT, Fujita-Fujiharu Y, Ishida H, Zhang Z, Nomura Y, Liu K, Uemura T, Sato Y, Ono M, Yamamoto M, Noda T, Shigematsu H, Drew D, Iwata S, Shimizu T, Nomura N, Ohto U
Nature (2022) 606 pp. 1021-1026 [ DOI: doi:10.1038/s41586-022-04845-4 Pubmed: 35580629 ]
- Complex of ntcp and fab (Complex from Mus musculus)
- Ntcp (Complex)
- Sodium/bile acid cotransporter (38 kDa, Protein from Rattus norvegicus)
- Fab (Complex from Rattus norvegicus)
- Fab heavy chain from antibody igg clone number yn69202 (26 kDa, Protein from Mus musculus)
- Fab light chain from antibody igg clone number yn69202 (24 kDa, Protein from Mus musculus)