6IU4
 
 | | Crystal structure of iron transporter VIT1 with cobalt ion | | Descriptor: | COBALT (II) ION, VIT1, ZINC ION | | Authors: | Kato, T, Nishizawa, T, Yamashita, K, Taniguchi, R, Kumazaki, K, Ishitani, R, Nureki, O. | | Deposit date: | 2018-11-27 | | Release date: | 2019-02-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Crystal structure of plant vacuolar iron transporter VIT1.
Nat Plants, 5, 2019
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6IU8
 | | Crystal structure of cytoplasmic metal binding domain with cobalt ions | | Descriptor: | COBALT (II) ION, VIT1, ZINC ION | | Authors: | Kato, T, Nishizawa, T, Yamashita, K, Kumazaki, K, Ishitani, R, Nureki, O. | | Deposit date: | 2018-11-27 | | Release date: | 2019-02-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of plant vacuolar iron transporter VIT1.
Nat Plants, 5, 2019
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6IU6
 | | Crystal structure of cytoplasmic metal binding domain with nickel ions | | Descriptor: | NICKEL (II) ION, VIT1, ZINC ION | | Authors: | Kato, T, Nishizawa, T, Yamashita, K, Kumazaki, K, Ishitani, R, Nureki, O. | | Deposit date: | 2018-11-27 | | Release date: | 2019-02-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Crystal structure of plant vacuolar iron transporter VIT1.
Nat Plants, 5, 2019
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6IU3
 | | Crystal structure of iron transporter VIT1 with zinc ions | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, VIT1, ZINC ION | | Authors: | Kato, T, Nishizawa, T, Yamashita, K, Taniguchi, R, Kumazaki, K, Ishitani, R, Nureki, O. | | Deposit date: | 2018-11-27 | | Release date: | 2019-02-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of plant vacuolar iron transporter VIT1.
Nat Plants, 5, 2019
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6IU9
 | | Crystal structure of cytoplasmic metal binding domain with iron ions | | Descriptor: | FE (II) ION, VIT1, ZINC ION | | Authors: | Kato, T, Nishizawa, T, Yamashita, K, Kumazaki, K, Ishitani, R, Nureki, O. | | Deposit date: | 2018-11-27 | | Release date: | 2019-02-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structure of plant vacuolar iron transporter VIT1.
Nat Plants, 5, 2019
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6IU5
 | | Crystal structure of cytoplasmic metal binding domain with zinc ions | | Descriptor: | CHLORIDE ION, VIT1, ZINC ION | | Authors: | Kato, T, Nishizawa, T, Yamashita, K, Kumazaki, K, Ishitani, R, Nureki, O. | | Deposit date: | 2018-11-27 | | Release date: | 2019-02-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Crystal structure of plant vacuolar iron transporter VIT1.
Nat Plants, 5, 2019
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6K9Q
 | | Structure of the native supercoiled hook as a universal joint | | Descriptor: | Flagellar hook protein FlgE | | Authors: | Kato, T, Miyata, T, Makino, F, Horvath, P, Namba, K. | | Deposit date: | 2019-06-17 | | Release date: | 2020-02-12 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Structure of the native supercoiled flagellar hook as a universal joint.
Nat Commun, 10, 2019
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7VR8
 | | Inward-facing structure of human EAAT2 in the substrate-free state | | Descriptor: | (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, CHOLESTEROL, ... | | Authors: | Kato, T, Kusakizako, T, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-10-22 | | Release date: | 2022-08-10 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (3.58 Å) | | Cite: | Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2.
Nat Commun, 13, 2022
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7VR7
 | | Inward-facing structure of human EAAT2 in the WAY213613-bound state | | Descriptor: | (2S)-2-azanyl-4-[[4-[2-bromanyl-4,5-bis(fluoranyl)phenoxy]phenyl]amino]-4-oxidanylidene-butanoic acid, (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, ... | | Authors: | Kato, T, Kusakizako, T, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-10-22 | | Release date: | 2022-08-10 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (3.49 Å) | | Cite: | Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2.
Nat Commun, 13, 2022
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7WLS
 | | Crystal structure of the multidrug efflux transporter BpeB from Burkholderia pseudomallei | | Descriptor: | Efflux pump membrane transporter, TETRAETHYLENE GLYCOL, UNDECYL-MALTOSIDE | | Authors: | Kato, T, Hung, L.-W, Yamashita, E, Okada, U, Terwilliger, T.C, Murakami, S. | | Deposit date: | 2022-01-13 | | Release date: | 2023-07-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.94 Å) | | Cite: | Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism.
Proc.Natl.Acad.Sci.USA, 120, 2023
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7WLV
 | | Crystal Structure of the Multidrug effulx transporter BpeF from Burkholderia pseudomallei. | | Descriptor: | DODECYL-BETA-D-MALTOSIDE, Efflux pump membrane transporter | | Authors: | Kato, T, Hung, L.-W, Yamashita, E, Okada, U, Terwilliger, T.C, Murakami, S. | | Deposit date: | 2022-01-13 | | Release date: | 2023-07-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism.
Proc.Natl.Acad.Sci.USA, 120, 2023
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6L63
 | | Human Coagulation Factor XIIa (FXIIa) bound with the macrocyclic peptide F3 containing two (1S,2S)-2-ACHC residues | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ACETYL GROUP, ... | | Authors: | Sengoku, T, Katoh, T, Hirata, K, Suga, H, Ogata, K. | | Deposit date: | 2019-10-26 | | Release date: | 2020-09-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic beta-amino acids.
Nat.Chem., 12, 2020
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7WDT
 | | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S | | Descriptor: | 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose, Beta-N-acetylhexosaminidase, ... | | Authors: | Yamada, C, Kashima, T, Fushinobu, S, Katoh, T, Katayama, T. | | Deposit date: | 2021-12-22 | | Release date: | 2022-12-28 | | Last modified: | 2023-06-14 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
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7WDU
 | | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with PUGNAc-6S | | Descriptor: | Beta-N-acetylhexosaminidase, CALCIUM ION, [[(3R,4R,5S,6R)-3-acetamido-4,5-bis(oxidanyl)-6-(sulfooxymethyl)oxan-2-ylidene]amino] N-phenylcarbamate | | Authors: | Kashima, T, Yamada, C, Fushinobu, S, Katoh, T, Katayama, T. | | Deposit date: | 2021-12-22 | | Release date: | 2022-12-28 | | Last modified: | 2023-06-14 | | Method: | X-RAY DIFFRACTION (2.23 Å) | | Cite: | A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
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3J0R
 | | Model of a type III secretion system needle based on a 7 Angstrom resolution cryoEM map | | Descriptor: | Protein mxiH | | Authors: | Fujii, T, Cheung, M, Blanco, A, Kato, T, Blocker, A.J, Namba, K. | | Deposit date: | 2011-11-03 | | Release date: | 2012-02-29 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (7.7 Å) | | Cite: | Structure of a type III secretion needle at 7-A resolution provides insights into its assembly and signaling mechanisms.
Proc.Natl.Acad.Sci.USA, 109, 2012
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6LKT
 | | Crystal structure of the Fab fragment of murine monoclonal antibody KH-1 against Human herpesvirus 6B | | Descriptor: | antibody Fab Fragment L-chain, antibody Fab fragment H chain | | Authors: | Nishimura, M, Novita, B.D, Kato, T, Tjan, L.H, Wang, B, Wakata, A, Poetranto, A.L, Kawabata, A, Tang, H, Aoshi, T, Mori, Y. | | Deposit date: | 2019-12-20 | | Release date: | 2020-06-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for the interaction of human herpesvirus 6B tetrameric glycoprotein complex with the cellular receptor, human CD134.
Plos Pathog., 16, 2020
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7D84
 | | 34-fold symmetry Salmonella S ring formed by full-length FliF | | Descriptor: | Flagellar M-ring protein | | Authors: | Kawamoto, A, Miyata, T, Makino, F, Kinoshita, M, Minamino, T, Imada, K, Kato, T, Namba, K. | | Deposit date: | 2020-10-07 | | Release date: | 2021-05-19 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries.
Nat Commun, 12, 2021
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1V7M
 | | Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab | | Descriptor: | Monoclonal TN1 Fab Heavy Chain, Monoclonal TN1 Fab Light Chain, Thrombopoietin | | Authors: | Feese, M.D, Tamada, T, Kato, Y, Maeda, Y, Hirose, M, Matsukura, Y, Shigematsu, H, Kato, T, Miyazaki, H, Kuroki, R. | | Deposit date: | 2003-12-18 | | Release date: | 2004-03-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.51 Å) | | Cite: | Structure of the receptor-binding domain of human thrombopoietin determined by complexation with a neutralizing antibody fragment
Proc.Natl.Acad.Sci.USA, 101, 2004
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1V7N
 | | Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab | | Descriptor: | Monoclonal TN1 Fab Heavy Chain, Monoclonal TN1 Fab Light Chain, Thrombopoietin | | Authors: | Feese, M.D, Tamada, T, Kato, Y, Maeda, Y, Hirose, M, Matsukura, Y, Shigematsu, H, Kato, T, Miyazaki, H, Kuroki, R. | | Deposit date: | 2003-12-18 | | Release date: | 2004-03-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Structure of the receptor-binding domain of human thrombopoietin determined by complexation with a neutralizing antibody fragment
Proc.Natl.Acad.Sci.USA, 101, 2004
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4D3E
 | | Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri | | Descriptor: | INVASIN IPAD | | Authors: | Cheung, M, Shen, D.-K, Makino, F, Kato, T, Roehrich, D, Martinez-Argudo, I, Walker, M.L, Murillo, I, Liu, X, Pain, M, Brown, J, Frazer, G, Mantell, J, Mina, P, Todd, T, Sessions, R.B, Namba, K, Blocker, A.J. | | Deposit date: | 2014-10-21 | | Release date: | 2014-12-10 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (24 Å) | | Cite: | Three-Dimensional Electron Microscopy Reconstruction and Cysteine-Mediated Crosslinking Provide a Model of the T3Ss Needle Tip Complex.
Mol.Microbiol., 95, 2015
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6LY9
 | | The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus | | Descriptor: | V-type ATP synthase subunit C, V-type ATP synthase subunit E, V-type ATP synthase subunit I, ... | | Authors: | Kishikawa, J, Nakanishi, A, Furuta, A, Kato, T, Namba, K, Tamakoshi, M, Mitsuoka, K, Yokoyama, K. | | Deposit date: | 2020-02-13 | | Release date: | 2020-09-09 | | Last modified: | 2020-09-30 | | Method: | ELECTRON MICROSCOPY (3.93 Å) | | Cite: | Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance.
Elife, 9, 2020
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6O97
 | | Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution | | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxyc yclohexyl 2-amino-2,4-dideoxy-4-propyl-alpha-D-glucopyranoside, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | | Authors: | Matsushita, T, Sati, G.C, Kondasinghe, N, Pirrone, M.G, Kato, T, Waduge, P, Kumar, H.S, Sanchon, A.C, Dobosz-Bartoszek, M, Shcherbakov, D, Juhas, M, Hobbie, S.N, Schrepfer, T, Chow, C.S, Polikanov, Y.S, Schacht, J, Vasella, A, Bottger, E.C, Crich, D. | | Deposit date: | 2019-03-13 | | Release date: | 2019-04-17 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens.
J. Am. Chem. Soc., 141, 2019
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8H4O
 | | Crystal Structure of nucleotide-free Irgb6_T95D mutant | | Descriptor: | T-cell-specific guanine nucleotide triphosphate-binding protein 2 | | Authors: | Saijo-Hamano, Y, Okuma, H, Sakai, N, Kato, T, Imasaki, T, Nitta, R. | | Deposit date: | 2022-10-11 | | Release date: | 2023-10-18 | | Last modified: | 2024-07-03 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I.
Genes Cells, 29, 2024
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6LTG
 | | Crystal structure of the Fab fragment of murine monoclonal antibody OHV-3 against Human herpesvirus 6B | | Descriptor: | MAGNESIUM ION, antibody Fab fragment H-chain, antibody Fab fragment L-chain | | Authors: | Nishimura, M, Novita, B.D, Kato, T, Tjan, L.H, Wang, B, Wakata, A, Poetranto, A.L, Kawabata, A, Tang, H, Aoshi, T, Mori, Y. | | Deposit date: | 2020-01-22 | | Release date: | 2020-06-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.63 Å) | | Cite: | Structural basis for the interaction of human herpesvirus 6B tetrameric glycoprotein complex with the cellular receptor, human CD134.
Plos Pathog., 16, 2020
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8HLB
 | | Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2 | | Descriptor: | TR109 heavy chain, TR109 light chain, TR92 heavy chain, ... | | Authors: | Akiba, H, Fujita, J, Ise, T, Nishiyama, K, Miyata, T, Kato, T, Namba, K, Ohno, H, Kamada, H, Nagata, S, Tsumoto, K. | | Deposit date: | 2022-11-29 | | Release date: | 2023-10-04 | | Method: | ELECTRON MICROSCOPY (3.63 Å) | | Cite: | Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection.
Commun Biol, 6, 2023
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