Cryo-EM structure of the aspartate:alanine antiporter AspT WT
Nanatani K, Kanno R, Kawabata T, Watanabe S, Hidaka M, Yamanaka T, Toda K, Fujiki T, Kunii K, Miyamoto A, Chiba F, Ogasawara S, Murata T, Humbel BM, Inaba K, Mitsuoka K, Guan L, Abe K, Yamamoto M, Koshiba S
To Be Published
- Aspartic acid (133 Da, Ligand)
- Aspartate:alanine antiporter aspt (58 kDa, Cellular component from Tetragenococcus halophilus)
- Aspartate/alanine antiporter (57 kDa, Protein from Tetragenococcus halophilus)
Cryo-EM structure of the head region of full-length ERGIC-53 with MCFD2 (form A)
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8jp4
Q-score: 0.496
Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K
Nat Commun (2024) 15 pp. 2404-2404 [ Pubmed: 38493152 DOI: doi:10.1038/s41467-024-46747-1 ]
- Calcium ion (40 Da, Ligand)
- Ergic-53-mcfd2 complex (Complex from Homo sapiens)
- Multiple coagulation factor deficiency protein 2 (13 kDa, Protein from Homo sapiens)
- Protein ergic-53 (58 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structures of the head region of full-length ERGIC-53 with MCFD2 (form B)
Resolution: 2.59 Å
EM Method: Single-particle
Fitted PDBs: 8jp5
Q-score: 0.476
Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K
Nat Commun (2024) 15 pp. 2404-2404 [ Pubmed: 38493152 DOI: doi:10.1038/s41467-024-46747-1 ]
- Calcium ion (40 Da, Ligand)
- Ergic-53-mcfd2 complex (Complex from Homo sapiens)
- Multiple coagulation factor deficiency protein 2 (13 kDa, Protein from Homo sapiens)
- Protein ergic-53 (58 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structures of the head region of full-length ERGIC-53 with MCFD2 (Substate A)
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8jp6
Q-score: 0.461
Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K
Nat Commun (2024) 15 pp. 2404-2404 [ Pubmed: 38493152 DOI: doi:10.1038/s41467-024-46747-1 ]
- Calcium ion (40 Da, Ligand)
- Ergic-53-mcfd2 complex (Complex from Homo sapiens)
- Multiple coagulation factor deficiency protein 2 (13 kDa, Protein from Homo sapiens)
- Protein ergic-53 (58 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the head region of full-length ERGIC-53 with MCFD2 (Substate B)
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8jp7
Q-score: 0.412
Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K
Nat Commun (2024) 15 pp. 2404-2404 [ Pubmed: 38493152 DOI: doi:10.1038/s41467-024-46747-1 ]
- Calcium ion (40 Da, Ligand)
- Ergic-53-mcfd2 complex (Complex from Homo sapiens)
- Multiple coagulation factor deficiency protein 2 (13 kDa, Protein from Homo sapiens)
- Protein ergic-53 (58 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the head region of full-length ERGIC-53 with MCFD2 (Substate C)
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8jp8
Q-score: 0.413
Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K
Nat Commun (2024) 15 pp. 2404-2404 [ Pubmed: 38493152 DOI: doi:10.1038/s41467-024-46747-1 ]
- Calcium ion (40 Da, Ligand)
- Ergic-53-mcfd2 complex (Complex from Homo sapiens)
- Multiple coagulation factor deficiency protein 2 (13 kDa, Protein from Homo sapiens)
- Protein ergic-53 (58 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the head region of full-length ERGIC-53 with MCFD2 (Substate D)
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8jp9
Q-score: 0.422
Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K
Nat Commun (2024) 15 pp. 2404-2404 [ Pubmed: 38493152 DOI: doi:10.1038/s41467-024-46747-1 ]
- Calcium ion (40 Da, Ligand)
- Ergic-53-mcfd2 complex (Complex from Homo sapiens)
- Multiple coagulation factor deficiency protein 2 (13 kDa, Protein from Homo sapiens)
- Protein ergic-53 (58 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of full-length ERGIC-53 with MCFD2
Resolution: 6.76 Å
EM Method: Single-particle
Fitted PDBs: 8jpg
Q-score: 0.143
Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K
Nat Commun (2024) 15 pp. 2404-2404 [ Pubmed: 38493152 DOI: doi:10.1038/s41467-024-46747-1 ]
- Calcium ion (40 Da, Ligand)
- Ergic-53-mcfd2 complex (Complex from Homo sapiens)
- Multiple coagulation factor deficiency protein 2 (13 kDa, Protein from Homo sapiens)
- Protein ergic-53 (58 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8j7u
Q-score: 0.412
Bui HB, Watanabe S, Nomura N, Liu K, Uemura T, Inoue M, Tsutsumi A, Fujita H, Kinoshita K, Kato Y, Iwata S, Kikkawa M, Inaba K
Nat Commun (2023) 14 pp. 4770-4770 [ DOI: doi:10.1038/s41467-023-40521-5 Pubmed: 37553324 ]
- Light chain of yn7114-08 fab (24 kDa, Protein from Mus musculus)
- Zinc transporter 7 (43 kDa, Protein from Homo sapiens)
- Heavy chain of yn7114-08 fab (24 kDa, Protein from Mus musculus)
- Human znt7-fab complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8j7w
Q-score: 0.496
Bui HB, Watanabe S, Nomura N, Liu K, Uemura T, Inoue M, Tsutsumi A, Fujita H, Kinoshita K, Kato Y, Iwata S, Kikkawa M, Inaba K
Nat Commun (2023) 14 pp. 4770-4770 [ DOI: doi:10.1038/s41467-023-40521-5 Pubmed: 37553324 ]
- Light chain of yn7114-08 fab (24 kDa, Protein from Mus musculus)
- Zinc transporter 7 (43 kDa, Protein from Homo sapiens)
- Heavy chain of yn7114-08 fab (24 kDa, Protein from Mus musculus)
- Human znt7-fab complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)